fixed broken data coordinate from PDB

data_multi_processor.py

@@ -88,14 +88,24 @@ def data_processing(path,id_name, atom_types, cutoff):
  l =[]
  with open(path_file, 'r') as f:
  for line in f:
- if line.startswith('ATOM') or line.startswith('TER'):
+ if line.startswith('ATOM'):
  clean_line = (line.rstrip()).split()
  #check for alignment mistakes within data, a row with spacing alignment error has 11 length after splitted by whitespace
  if len(clean_line) == 11:
  #split the 2nd last column by the 4th index (this inference is according to PDB file formatting)
  split = [clean_line[-2][:4], clean_line[-2][4:]]
  clean_line[-2] = split[1]
  clean_line.insert(-2, split[0])
+ #check if coordinate data collumns are collided (most likely happens between x and y coor)
+ if len(clean_line[6])>=13:
+ split = [clean_line[6][:-8], clean_line[6][-8:]]
+ last_elem = clean_line.pop()
+ clean_line[-1] = last_elem
+ clean_line.insert(6, split[0])
+ clean_line[7] = split[1]
+ l.append(clean_line)
+ elif line.startswith('TER'):
+ clean_line = (line.rstrip()).split()
  l.append(clean_line)
  elif line.startswith('ENDMDL'):
  break
@@ -160,14 +170,24 @@ def data_multi_processing(path,id_name, atom_types, cutoff, pool):
  l =[]
  with open(path_file, 'r') as f:
  for line in f:
- if line.startswith('ATOM') or line.startswith('TER'):
+ if line.startswith('ATOM'):
  clean_line = (line.rstrip()).split()
  #check for alignment mistakes within data, a row with spacing alignment error has 11 length after splitted by whitespace
  if len(clean_line) == 11:
  #split the 2nd last column by the 4th index (this inference is according to PDB file formatting)
  split = [clean_line[-2][:4], clean_line[-2][4:]]
  clean_line[-2] = split[1]
  clean_line.insert(-2, split[0])
+ #check if coordinate data collumns are collided (most likely happens between x and y coor)
+ if len(clean_line[6])>=13:
+ split = [clean_line[6][:-8], clean_line[6][-8:]]
+ last_elem = clean_line.pop()
+ clean_line[-1] = last_elem
+ clean_line.insert(6, split[0])
+ clean_line[7] = split[1]
+ l.append(clean_line)
+ elif line.startswith('TER'):
+ clean_line = (line.rstrip()).split()
  l.append(clean_line)
  elif line.startswith('ENDMDL'):
  break
@@ -197,14 +217,24 @@ def data_multi_processing_mp(params):
  l =[]
  with open(path_file, 'r') as f:
  for line in f:
- if line.startswith('ATOM') or line.startswith('TER'):
+ if line.startswith('ATOM'):
  clean_line = (line.rstrip()).split()
  #check for alignment mistakes within data, a row with spacing alignment error has 11 length after splitted by whitespace
  if len(clean_line) == 11:
  #split the 2nd last column by the 4th index (this inference is according to PDB file formatting)
  split = [clean_line[-2][:4], clean_line[-2][4:]]
  clean_line[-2] = split[1]
  clean_line.insert(-2, split[0])
+ #check if coordinate data collumns are collided (most likely happens between x and y coor)
+ if len(clean_line[6])>=13:
+ split = [clean_line[6][:-8], clean_line[6][-8:]]
+ last_elem = clean_line.pop()
+ clean_line[-1] = last_elem
+ clean_line.insert(6, split[0])
+ clean_line[7] = split[1]
+ l.append(clean_line)
+ elif line.startswith('TER'):
+ clean_line = (line.rstrip()).split()
  l.append(clean_line)
  elif line.startswith('ENDMDL'):
  break
@@ -267,7 +297,7 @@ def unit_test_y_data():
 # print(len(complex_files))
 # 
 ## test_file = path+'/'+complex_files[2]
-# test_file = path+'/2wy2.ent.pdb'
+# test_file = path+'/1f5r.ent.pdb'
 # print(test_file)
 # 
 # '''
@@ -276,20 +306,33 @@ def unit_test_y_data():
 # l =[]
 # with open(test_file, 'r') as f:
 # for line in f:
-# if line.startswith('ATOM') or line.startswith('TER'):
+# if line.startswith('ATOM'):
 # clean_line = (line.rstrip()).split()
 # #check for alignment mistakes within data, a row with spacing alignment error has 11 length after splitted by whitespace
 # if len(clean_line) == 11:
 # #split the 2nd last column by the 4th index (this inference is according to PDB file formatting)
 # split = [clean_line[-2][:4], clean_line[-2][4:]]
 # clean_line[-2] = split[1]
 # clean_line.insert(-2, split[0])
+# #check if coordinate data collumns are collided (most likely happens between x and y coor)
+# if len(clean_line[6])>=13:
+# split = [clean_line[6][:-8], clean_line[6][-8:]]
+# last_elem = clean_line.pop()
+# clean_line[-1] = last_elem
+# clean_line.insert(6, split[0])
+# clean_line[7] = split[1]
+# l.append(clean_line)
+# elif line.startswith('TER'):
+# clean_line = (line.rstrip()).split()
 # l.append(clean_line)
 # elif line.startswith('ENDMDL'):
 # break
 # df_atoms = (pd.DataFrame(l)).rename(columns={0:'record', 6:'x_coor', 7:'y_coor', 8:'z_coor', 11:'atom_type'})
-# 
-#
+# for i in range(len(l)):
+# print(i, l[i])
+# 
+# print(l[2013])
+# print(len(l[293][6].split('-')))
 # print(df_atoms)
 # 
 # '''
@@ -303,7 +346,8 @@ def unit_test_y_data():
 # 
 # print(df_atoms.index[df_atoms['record'] == 'TER'].tolist())
 # print(l_df)
-
+# 
+# print(df_atoms.iloc[293])
  '''
  multiprocessing unit test
  '''
@@ -351,6 +395,7 @@ def unit_test_y_data():
  #initialize parameters
  path = 'C:/Users/beryl/Documents/Computational Science/Kanazawa/Thesis/Dataset/PP'
  complex_files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f))]
+ #print(complex_files)
 
  atom_types = ['C','N','O','F','P','S','Cl','Br','I']
  cutoff = 12
@@ -415,5 +460,5 @@ def unit_test_y_data():
  except FileNotFoundError:
  print('File is not found')
  saved_ids = [d['id'] for d in data]
- print('processed protein IDs = ',saved_ids)
+ print('processed protein IDs = ',saved_ids, print(len(saved_ids)))