added feature extraction scheme

driver.py

@@ -10,6 +10,7 @@
 import feature_calculator as fc
 import time
 import multiprocessing
+import pickle
 
 if __name__=="__main__":
  import json
@@ -20,18 +21,59 @@
  y_path = conf['index']['PP'] 
 
  complex_files = pdbp.list_files(x_path)
- id_name = complex_files[1]
- test_file = x_path+"/"+id_name
- chains = pdbp.loader_pdbbind(test_file) 
+# id_name = complex_files[1]
+# test_file = x_path+"/"+id_name
+# chains = pdbp.loader_pdbbind(test_file) 
  atom_types = ['C','N','O','S']
  cutoff = 12
 
- print(chains, len(chains))
+# print(chains, len(chains))
  start_time = time.time()
  pool = multiprocessing.Pool() 
 
- x_vec = fc.x_processor_mp([chains, id_name, atom_types, cutoff, pool])
- print(x_vec)
+# x_vec = fc.x_processor_mp([chains, id_name, atom_types, cutoff, pool])
+# print(x_vec)
 
+ filename = "dataset_mini_HPC.pkl"
+ #y_data loader
+ df_y = fc.y_processor(conf['index']['PP'])
+
+ #check if id is already existed within file, if yes, skip it
+ data = []
+ try:
+ with open(filename, 'rb') as fr:
+ print(filename, 'is found')
+ try:
+ while True:
+ data.append(pickle.load(fr))
+ except EOFError:
+ pass 
+ except FileNotFoundError:
+ print('File is not found')
+ saved_ids = [d['id'] for d in data]
+
+ #process and save the data
+ try:
+ i=0
+ for id_name in complex_files:
+ if id_name in saved_ids:
+ continue
+ else:
+ print("start of process for ID :",id_name)
+ pathfile = x_path+"/"+id_name
+ chains = pdbp.loader_pdbbind(pathfile) 
+ vector = fc.x_processor_mp([chains, id_name, atom_types, cutoff, pool])
+ y = df_y.loc[df_y['id']==id_name.split('.')[0]]['log_y'].values[0]
+ vector["y"]=y
+ print("ID : ", id_name)
+ print('value of x vector (R^N) = ', vector)
+ with open(filename, 'ab') as f:
+ pickle.dump(vector, f)
+ i+=1
+ except KeyboardInterrupt:
+ print('interrupted !!')
+
  end_time = time.time()
- print('time elapsed =',end_time-start_time,'seconds')
+ print("the number of protein processed in current run = ",i)
+ print('time elapsed =',end_time-start_time,'seconds')
+