Updates

Test/test_ddg.py → Evaluation/test_ddg.py

@@ -56,7 +56,7 @@ gemme_jet_dict = load_obj('./comp_mut_map_gemme_jet')
 
 model_s = load_model(path.join('../Models','DLA_Mutation_model'))
 
-backrub_models = glob.glob(path.join('../Examples', 'map_dir_mut'))
+backrub_models = glob.glob(path.join('../Examples', 'map_dir_mut', '*', '*'))
 backrub_models_test = []
 for br_model in backrub_models:
     comp = path.basename(br_model)[:4]

Evaluation/test_xray.py

@@ -117,7 +117,7 @@ def load_map(sample_test):
     remove(sample_test.replace('.lz4',''))
     return X, y, reg_type, res_pos, res_name, inter_info
         
-samples = glob.glob(path.join(map_dir,'*','1','*'))
+samples = glob.glob(path.join(map_dir,'*','*'))
 
 
 output_handler = open(output_file, 'w')

Evaluation/test_xray_4channels.py

@@ -121,7 +121,7 @@ def load_map(sample_test):
     remove(sample_test.replace('.lz4',''))
     return X, y, reg_type, res_pos, res_name, inter_info
         
-samples = glob.glob(path.join(map_dir,'*','1','*'))
+samples = glob.glob(path.join(map_dir,'*','*'))
 
 
 output_handler = open(output_file, 'w')

Evaluation/testing_backrub.py

@@ -123,7 +123,7 @@ def load_map(sample_test):
     #return X, y, y_ddg
     return X, y, y_ddg, region, comp_type, expr_method
         
-samples = glob.glob(path.join(map_dir,'*','1','*'))
+samples = glob.glob(path.join(map_dir,'*','*'))
 
 
 output_handler = open(output_file, 'w')

Evaluation/testing_backrub_4channels.py

@@ -123,7 +123,7 @@ def load_map(sample_test):
     #return X, y, y_ddg
     return X, y, y_ddg, region, comp_type, expr_method
         
-samples = glob.glob(path.join(map_dir,'*','1','*'))
+samples = glob.glob(path.join(map_dir,'*','*'))
 
 
 output_handler = open(output_file, 'w')

README.md

@@ -139,7 +139,7 @@ Example
 
 - From ```Representation``` run ```python generate_cubes_ddg.py```. It extracts cubic volumetric maps around the mutation positions from both wild-type and mutant complexes.
 
-- From ```Test``` run ```python test_ddg.py```. The output contains the values of predicted and experimental values of ΔΔG.
+- From ```Evaluation``` run ```python test_ddg.py```. The output contains the values of predicted and experimental values of ΔΔG.
 
 ### Downstream tasks
 

Representation/generate_cubes_interface.py

@@ -163,14 +163,9 @@ def process_targetcomplex(targetcomplex, comp_dir, report_dict):
         if targetcomplex in already_exist:
             return
         logging.info('Processing ' + targetcomplex + ' ...')
-        pos_path = path.join(map_dir, targetcomplex, '1')
-        neg_path = path.join(map_dir, targetcomplex, '0')
+
         if not path.exists(path.join(map_dir, targetcomplex)):
             mkdir(path.join(map_dir, targetcomplex))
-        if not path.exists(pos_path):
-            mkdir(pos_path)    
-        if not path.exists(neg_path):
-            mkdir(neg_path)
 
         ch1, ch2 =  comp_dict.loc[comp_dict.Comp == targetcomplex][['ch1','ch2']].iloc[0]
         
@@ -184,7 +179,7 @@ def process_targetcomplex(targetcomplex, comp_dir, report_dict):
 def manage_pair_files(use_multiprocessing):
     tc_cases = []
     for tc in target_comp:
-        tc_cases.append((tc, comp_dir))
+        tc_cases.append((tc.replace('.pdb',''), comp_dir))
     report_dict = tl.do_processing(tc_cases, process_targetcomplex, use_multiprocessing)
     return report_dict
 

Representation/generate_cubes_reduce_channels_multiproc.py

@@ -84,7 +84,7 @@ for i,a in enumerate(all_channels):
     if a[0] == "S":
         S_index.append(i)
         
-samples= glob.glob(path.join('../Examples/map_dir','*','*','*.lz4'))
+samples= glob.glob(path.join('../Examples/map_dir','*','*.lz4'))
 
 
 def process_sample(sample, report_dict):