Push corrected version

HInt.txt

@@ -1,8 +1,8 @@
 ###Informations  #All arguments are optional
 Signal_peptide : Yes #Yes, No or None.
 DeepLoc : Periplasmic, Extracellular
-Max_protein_lenght :
-Min_protein_lenght :
+Max_protein_length :
+Min_protein_length :
 Homo-oligomer : #Integer between 2-20
 Interact_with : P33790 #UniprotID/Protein Name
 Organism : gram- #gram-, gram+, euk, arch or None

HInt/File_proteins.py

@@ -43,7 +43,7 @@ def set_proteins_sequence_SP (self, new_protein_sequence) :
 
     def set_proteins_sequence_no_SP (self, new_protein_sequence) :
         """
-        Sets a dict of all sequences without Signal peptide and set a lenght dict.
+        Sets a dict of all sequences without Signal peptide and set a length dict.
 
         Parameters:
         ----------
@@ -53,7 +53,7 @@ def set_proteins_sequence_no_SP (self, new_protein_sequence) :
         ----------
         """
         self.protein_sequence_no_SP = new_protein_sequence
-        self.find_prot_lenght(new_protein_sequence)
+        self.find_prot_length(new_protein_sequence)
 
     def set_proteins (self, new_protein) :
         """
@@ -81,18 +81,18 @@ def set_file_name (self, filename) :
         """
         self.file_name = filename
 
-    def set_lenght_prot (self, lenght_prot) :
+    def set_length_prot (self, length_prot) :
         """
-        Sets lenght of all proteins.
+        Sets length of all proteins.
 
         Parameters:
         ----------
-        lenght_prot = dictionary
+        length_prot = dictionary
 
         Returns:
         ----------
         """
-        self.lenght_prot = lenght_prot
+        self.length_prot = length_prot
 
     def set_result_dict (self, result_dict) :
         """
@@ -264,18 +264,18 @@ def get_file_name (self) :
         """
         return self.file_name
 
-    def get_lenght_prot (self) :
+    def get_length_prot (self) :
         """
-        Return the lenght of proteins.
+        Return the length of proteins.
 
         Parameters:
         ----------
 
         Returns:
         ----------
-        lenght_prot : dictionary
+        length_prot : dictionary
         """
-        return self.lenght_prot
+        return self.length_prot
 
     def get_result_dict (self) :
         """
@@ -724,7 +724,7 @@ def Make_save_dict (self) :
         with open('log_file/save_dict.pkl', 'wb') as out_file :
             pickle.dump(pkl_dict, out_file)
 
-    def find_prot_lenght (self, prot_dict = None) :
+    def find_prot_length (self, prot_dict = None) :
         """
         Compute and store the length (number of amino acids) of each protein based on sequences without signal peptides.
 
@@ -737,10 +737,10 @@ def find_prot_lenght (self, prot_dict = None) :
         else :
             proteins = prot_dict
         sequences = self.get_proteins_sequence_no_SP()
-        lenght_prot = dict()
+        length_prot = dict()
         for protein in proteins :
-            lenght_prot[protein] = len(sequences[protein])
-        self.set_lenght_prot(lenght_prot)
+            length_prot[protein] = len(sequences[protein])
+        self.set_length_prot(length_prot)
 
 
     def create_fasta_file (self, with_SP, need_msa=[], need_pkl=[]) :

HInt/HInt.py

@@ -88,7 +88,7 @@ def main() :
     HInt_object = File_proteins(Informations_dict["Path_Uniprot_ID"], Informations_dict["Interact_with"], Informations_dict["AlphaFold"])
 
     time_dict = HInt_object.get_time_dict() 
-    time_dict["Summarize_info"] = [Informations_dict["Interact_with"], Informations_dict["DeepLoc"], Informations_dict["Signal_peptide"], Informations_dict["Min_protein_lenght"], Informations_dict["Max_protein_lenght"], Informations_dict["Homo-oligomer"],str(len(HInt_object.get_possible_prey())),Informations_dict["Organism"]]
+    time_dict["Summarize_info"] = [Informations_dict["Interact_with"], Informations_dict["DeepLoc"], Informations_dict["Signal_peptide"], Informations_dict["Min_protein_length"], Informations_dict["Max_protein_length"], Informations_dict["Homo-oligomer"],str(len(HInt_object.get_possible_prey())),Informations_dict["Organism"]]
 
     logger.info("GPUs set to: %s", GPU)
     logger.info("Number of CPUs set to: %s", CPU)
@@ -116,7 +116,7 @@ def main() :
 
     # Filter proteins based on sequence length
     # (default: remove proteins shorter than 20 AA)
-    need_msa, need_pkl, need_DeepLoc = filter_lenght(HInt_object, Informations_dict, need_msa, need_pkl, need_DeepLoc)
+    need_msa, need_pkl, need_DeepLoc = filter_length(HInt_object, Informations_dict, need_msa, need_pkl, need_DeepLoc)
 
     # --------------------------------------------------------------
     # DeepLoc filtering
@@ -159,11 +159,11 @@ def main() :
 
     for bait in Informations_dict["Interact_with"] : # Adjust bait protein lengths if specific regions are defined
         if Informations_dict["Regions"][bait] != "0-0" :
-            dict_lenght = HInt_object.get_lenght_prot()
+            dict_length = HInt_object.get_length_prot()
             start = int(Informations_dict["Regions"][bait].split("-")[0])
             end = int(Informations_dict["Regions"][bait].split("-")[1])
-            dict_lenght[bait] = end - start + 1
-            HInt_object.set_lenght_prot(dict_lenght)
+            dict_length[bait] = end - start + 1
+            HInt_object.set_length_prot(dict_length)
 
 
     # Filter proteins based on signal peptide criteria

HInt/Scoring_HInt.py

@@ -413,13 +413,13 @@ def Create_figures (file, Informations_dict, AF_version, sorted_proteins, CPU) :
     regions = Informations_dict["Regions"]
     possible_prey = file.get_possible_prey()
     result_dict = file.get_result_dict()
-    complete_lenght_prot = file.get_lenght_prot()
+    complete_length_prot = file.get_length_prot()
     complete_seq_prot = file.get_proteins_sequence_no_SP()
 
     interface_dict = dict()
     tasks = []
     baits_seq = {}
-    baits_lenght = {}
+    baits_length = {}
     for baits in Informations_dict["Multimer_bait"] :
         bait_file = baits
         for bait in baits.split(",") :
@@ -428,15 +428,15 @@ def Create_figures (file, Informations_dict, AF_version, sorted_proteins, CPU) :
                 end = int(regions[bait].split("-")[1])
                 bait_file = bait_file.replace(bait,f"{bait}_{start}-{end}")
             baits_seq [bait] = complete_seq_prot[bait]
-            baits_lenght [bait] = complete_lenght_prot[bait]
+            baits_length [bait] = complete_length_prot[bait]
         bait_file = bait_file.replace(",","_and_")
         for prey in possible_prey :
-            lenght_prot = copy.deepcopy(baits_lenght)
-            lenght_prot [prey] = complete_lenght_prot[prey]
+            length_prot = copy.deepcopy(baits_length)
+            length_prot [prey] = complete_length_prot[prey]
             seq_prot = copy.deepcopy(baits_seq)
             seq_prot [prey] = complete_seq_prot[prey]
             if "Reason_for_filtering" not in result_dict[prey].keys() : #only for validate preys
-                tasks.append((AF_version, bait_file, prey, lenght_prot, seq_prot, baits, regions))
+                tasks.append((AF_version, bait_file, prey, length_prot, seq_prot, baits, regions))
     if tasks : #if there is interaction to process            
         with Pool(processes=CPU) as pool :
             results_res_int = pool.map(postprocess_interaction, tasks)
@@ -466,7 +466,7 @@ def postprocess_interaction (args) : #maybe split first and second part of funct
     ----------
     interface_dict : dict
     """
-    (AF_version, bait_file, prey, lenght_prot, seq_prot, baits, region) = args
+    (AF_version, bait_file, prey, length_prot, seq_prot, baits, region) = args
     if os.path.isdir (f"./result_PPI_int/{bait_file}_and_{prey}") == True :
         outdir = f"./result_PPI_int/{bait_file}_and_{prey}"
     if os.path.isdir (f"./result_PPI_int/{prey}_and_{bait_file}") == True :
@@ -475,7 +475,7 @@ def postprocess_interaction (args) : #maybe split first and second part of funct
     if AF_version == "2" :
         plot_Distogram(outdir)
 
-    residues_at_interface, proteins, path_int, color_res = make_table_res_int(lenght_prot, seq_prot, outdir, baits, prey, AF_version, region)
+    residues_at_interface, proteins, path_int, color_res = make_table_res_int(length_prot, seq_prot, outdir, baits, prey, AF_version, region)
 
     if residues_at_interface is not None :
         color_int_residues(path_int, color_res, proteins)
@@ -549,7 +549,7 @@ def plot_Distogram (job) :
             logger.info(f"Distogram created for {job}")
 
 
-def make_table_res_int (lenght_prot, seq_prot, path_int, baits, prey, AF_version, regions) :
+def make_table_res_int (length_prot, seq_prot, path_int, baits, prey, AF_version, regions) :
     """
     Generate a detailed table of residue-residue interactions for a protein-protein complex.
 
@@ -559,7 +559,7 @@ def make_table_res_int (lenght_prot, seq_prot, path_int, baits, prey, AF_version
 
     Parameters :
     ----------
-    lenght_prot : dict
+    length_prot : dict
     seq_prot : dict
     path_int : str
     baits : str
@@ -612,16 +612,16 @@ def make_table_res_int (lenght_prot, seq_prot, path_int, baits, prey, AF_version
             del logits
             del bin_edges
             gc.collect()
-            complete_lenght = 0
+            complete_length = 0
             max_hori_index = 0
             for bait in baits.split(",") :
-                complete_lenght += lenght_prot[bait]
+                complete_length += length_prot[bait]
             for bait in baits.split(",") :
                 min_hori_index = max_hori_index
-                max_hori_index += lenght_prot[bait]
+                max_hori_index += length_prot[bait]
                 bait_prey = bait +"_and_" + proteins[-1]
                 dict_int[bait_prey] = [[bait," "+proteins[-1]," Distance_Ä"," PAE_score"]]
-                for line in range(complete_lenght,complete_lenght+lenght_prot[proteins[-1]]) :
+                for line in range(complete_length,complete_length+length_prot[proteins[-1]]) :
                     hori_index = -1
                     for distance in dist[line] :
                         hori_index += 1
@@ -633,10 +633,10 @@ def make_table_res_int (lenght_prot, seq_prot, path_int, baits, prey, AF_version
                                     if regions[bait] != "0-0" : #if region selected, need to ajust index
                                         res_in_tot_seq = hori_index - min_hori_index + int(regions[bait].split("-")[0]) - 1
                                     residue1 = seq_prot[bait][res_in_tot_seq]
-                                    residue2 = seq_prot[proteins[-1]][line-complete_lenght]
-                                    dict_int[bait_prey].append([residue1+":"+str(res_in_tot_seq+1)," "+residue2+":"+str(line-complete_lenght+1)," "+str(distance), " "+str(pae_mtx[line][real_hori_index])])
+                                    residue2 = seq_prot[proteins[-1]][line-complete_length]
+                                    dict_int[bait_prey].append([residue1+":"+str(res_in_tot_seq+1)," "+residue2+":"+str(line-complete_length+1)," "+str(distance), " "+str(pae_mtx[line][real_hori_index])])
                                     color_res[bait].add(str(res_in_tot_seq+1))
-                                    color_res[proteins[-1]].add(str(line-complete_lenght+1))
+                                    color_res[proteins[-1]].add(str(line-complete_length+1))
             del dist
             del pae_mtx
             gc.collect()
@@ -651,7 +651,7 @@ def make_table_res_int (lenght_prot, seq_prot, path_int, baits, prey, AF_version
         PAE_CUTOFF  = 10.0 #Observation: PAE value for residue at the interaciotn of AF3 model is generally lower than AF2 model
         ATOM_CONTACT = ["C","CA","CB"]
 
-        len_chain_last = lenght_prot[proteins[-1]]
+        len_chain_last = length_prot[proteins[-1]]
         total_len = pae_mtx.shape[0]
         int_already_know = {}
         structure = parser.get_structure('protein',os.path.join(path_int, f"{names_int}_ranked_0.pdb"))