Fast-HInt-ppi 0.1.9__tar.gz → 0.2.1__tar.gz

{fast_hint_ppi-0.1.9 → fast_hint_ppi-0.2.1}/Fast_HInt/Scoring_HInt.py

@@ -63,7 +63,7 @@ def Score_interaction (file, Informations_dict, CPU, Interaction, job="", multi_
     result_dict = file.get_result_dict()
     int_score = file.get_int_score() #saved scores
     homo_score = file.get_homo_score()
-    new_possible_prey = list()
+    new_possible_prey = file.get_possible_prey()
     Path_ccp4 = Informations_dict["Path_ccp4"]
     regions = Informations_dict["Regions"]
     nbr_homo = Informations_dict["Homo-oligomer"]
@@ -85,7 +85,6 @@ def Score_interaction (file, Informations_dict, CPU, Interaction, job="", multi_
     if not exists :
         subprocess.run([tool, "create", "-y", "-n", "pi_score","python=2.7", "scikit-learn=0.20.4", "biopython", "biopandas"], check=True)
 
-
     if bait != "" and job == "" : #setup bait name
         bait_name = bait.replace(";","_and_")
         for prot in bait.split(";") :
@@ -94,8 +93,8 @@ def Score_interaction (file, Informations_dict, CPU, Interaction, job="", multi_
                 end = int(regions[prot].split("-")[1])
                 bait_name = bait_name.replace(prot,f"{prot}_{start}-{end}")
         possible_prey = file.get_possible_prey()
-        
     if job != "" :
+        print("why")
         bait = job.replace(job.split(";")[-1],"").strip(";")
         bait_name = bait.replace(";","_and_")
         possible_prey = [job.split(";")[-1].strip("\n")]
@@ -104,7 +103,7 @@ def Score_interaction (file, Informations_dict, CPU, Interaction, job="", multi_
                 start = int(regions[prot].split("-")[0])
                 end = int(regions[prot].split("-")[1])
                 bait_name = bait_name.replace(prot,f"{prot}_{start}-{end}")
-        
+    
     #Multiprocessing to score all interactions
     if os.path.isdir(f"./result_{Interaction}") == True :
         if Interaction == "homo_int" : #for homo-oligomer
@@ -113,9 +112,10 @@ def Score_interaction (file, Informations_dict, CPU, Interaction, job="", multi_
                     ppi_list.append(f"./result_{Interaction}/{protein}_homo_{nbr_homo}er") #Found a solution for score only homo-oligomer without score
                 else :
                     result_dict[protein][f"hiQ_score_{nbr_homo}er"] = homo_score[protein][f"hiQ_score_{nbr_homo}er"]
-                    if homo_score[protein][f"hiQ_score_{nbr_homo}er"] > 0 :
-                        new_possible_prey.append(protein)
+                    #if homo_score[protein][f"hiQ_score_{nbr_homo}er"] > 0 :
+                    #    new_possible_prey.append(protein)
                     if homo_score[protein][f"hiQ_score_{nbr_homo}er"] == 0 :
+                        new_possible_prey.remove(protein)
                         result_dict[protein]["Reason_for_filtering"] = f"Bad homo-oligomer PAE : AF"
         if Interaction == "PPI_int" : #for one vs all
             for protein in possible_prey : #check if protein is already score
@@ -128,9 +128,10 @@ def Score_interaction (file, Informations_dict, CPU, Interaction, job="", multi_
                         ppi_list.append(f"./result_{Interaction}/{protein}_and_{bait_name}")
                 else :
                     result_dict[protein][f"iQ_score_vs_{bait_name}"] = int_score[protein][f"iQ_score_vs_{bait_name}"]
-                    if int_score[protein][f"iQ_score_vs_{bait_name}"] > 0 :
-                        new_possible_prey.append(protein)
+                    #if int_score[protein][f"iQ_score_vs_{bait_name}"] > 0 :
+                    #    new_possible_prey.append(protein)
                     if int_score[protein][f"iQ_score_vs_{bait_name}"] == 0 :
+                        new_possible_prey.remove(protein)
                         result_dict[protein]["Reason_for_filtering"] = f"Bad interactions with {bait_name} : inter PAE > 10 A"
         if Interaction == "Compounds" : #for compounds
             for compound in Compounds :

{fast_hint_ppi-0.1.9 → fast_hint_ppi-0.2.1}/Fast_HInt/Utils_HInt.py

@@ -477,7 +477,7 @@ def create_feature (file, Informations_dict, GPU, CPU, need_msa, need_pkl) :
                 msa_name = f"./log_file/{protein}_msa.fasta"
                 cmd = ["create_individual_features.py",
                 f"--fasta_paths={msa_name}",
-                f"--data_dir=/data/alphadata_v2",
+                f"--data_dir={Path_AlphaFold_Data}",
                 "--save_msa_files=True",
                 f"--output_dir={Path_Pickle_Feature}",
                 "--max_template_date=2024-05-02",
@@ -940,7 +940,8 @@ def Generate_first_batch(job_with_vram_length, GPU, multi_job_per_gpu) :
     pynvml.nvmlInit()
     handle = pynvml.nvmlDeviceGetHandleByIndex(int(GPU[0]))
     mem_info = pynvml.nvmlDeviceGetMemoryInfo(handle)
-    vram = (mem_info.total / 1024**2) * 0.001  # GiB    pynvml.nvmlShutdown()
+    vram = (mem_info.total / 1024**2) * 0.001  # GiB 
+    pynvml.nvmlShutdown()
     gpu_vram_used = {gpu: 0.0 for gpu in GPU}
     gpu_jobs = []
 
@@ -956,7 +957,7 @@ def Generate_first_batch(job_with_vram_length, GPU, multi_job_per_gpu) :
 
         for gpu_id in sorted_gpus :
 
-            free = max_vram - gpu_vram_used[gpu_id]
+            free = vram - gpu_vram_used[gpu_id]
 
             if job_vram <= free and (multi_job_per_gpu or len(gpu_jobs[gpu_id]) == 0) :
 

{fast_hint_ppi-0.1.9 → fast_hint_ppi-0.2.1}/Fast_HInt_ppi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Fast_HInt-ppi
-Version: 0.1.9
+Version: 0.2.1
 Summary: A tool to find homologous interactions and speed up AlphaFold-based structural modeling.
 Home-page: https://github.com/Qrouger/HInt
 Author: Quentin Rouger

{fast_hint_ppi-0.1.9 → fast_hint_ppi-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Fast_HInt-ppi
-Version: 0.1.9
+Version: 0.2.1
 Summary: A tool to find homologous interactions and speed up AlphaFold-based structural modeling.
 Home-page: https://github.com/Qrouger/HInt
 Author: Quentin Rouger

{fast_hint_ppi-0.1.9 → fast_hint_ppi-0.2.1}/setup.py

@@ -4,7 +4,7 @@ from setuptools import setup
 
 setup(
     name='Fast_HInt-ppi',
-    version='0.1.9',
+    version='0.2.1',
     description=(
         'A tool to find homologous interactions and speed up AlphaFold-based structural modeling.'
     ),