fatmacankara commited on
Commit
1b166bd
·
1 Parent(s): 9058c14

Update code/pdb_featureVector.py

Browse files
Files changed (1) hide show
  1. code/pdb_featureVector.py +5 -9
code/pdb_featureVector.py CHANGED
@@ -40,9 +40,9 @@ from add_alignment import *
40
  from manage_files import *
41
  from add_3Dalignment import *
42
  from add_sasa import *
43
- from standard import standardize
44
- from standard import finalTouch
45
  from add_interface_pos import *
 
46
  from utils import *
47
  from pdbMapping import *
48
  from uniprotSequenceMatch import uniprotSequenceMatch
@@ -309,7 +309,6 @@ def pdb(input_set, mode, impute):
309
 
310
  print('Extracting interface residues...\n')
311
  data_interface = pd.read_csv(path_to_interfaces, sep='\t')
312
-
313
 
314
  positions = get_interface_positions(data_interface, 'P1', 'P2')
315
 
@@ -318,15 +317,10 @@ def pdb(input_set, mode, impute):
318
  for key, val in positions.items():
319
  k = pd.Series((key, str(list(set(val)))))
320
  interface_dataframe = interface_dataframe.append(k, ignore_index=True)
321
-
322
  interface_dataframe.columns = ['uniprotID', 'positions']
323
- st.write('HERE')
324
  data = finalTouch(allData)
325
- st.write('finalTouch')
326
- st.write(data.head())
327
  data = data.merge(interface_dataframe, on='uniprotID', how='left')
328
  data.positions = data.positions.astype('str')
329
- st.write('passed')
330
  for i in data.index:
331
  if (str(data.at[i, 'pos']) in data.at[i, 'positions']) and data.at[i, 'trsh4'] == 'surface':
332
  data.at[i, 'threeState_trsh4_HQ'] = 'interface'
@@ -465,4 +459,6 @@ def pdb(input_set, mode, impute):
465
  minutes, seconds = divmod(rem, 60)
466
  print("Time passed: {:0>2}:{:0>2}:{:05.2f}".format(int(hours), int(minutes), seconds))
467
  #sys.stdout.close()
468
- return data
 
 
 
40
  from manage_files import *
41
  from add_3Dalignment import *
42
  from add_sasa import *
43
+ from standard import *
 
44
  from add_interface_pos import *
45
+ from standard import *
46
  from utils import *
47
  from pdbMapping import *
48
  from uniprotSequenceMatch import uniprotSequenceMatch
 
309
 
310
  print('Extracting interface residues...\n')
311
  data_interface = pd.read_csv(path_to_interfaces, sep='\t')
 
312
 
313
  positions = get_interface_positions(data_interface, 'P1', 'P2')
314
 
 
317
  for key, val in positions.items():
318
  k = pd.Series((key, str(list(set(val)))))
319
  interface_dataframe = interface_dataframe.append(k, ignore_index=True)
 
320
  interface_dataframe.columns = ['uniprotID', 'positions']
 
321
  data = finalTouch(allData)
 
 
322
  data = data.merge(interface_dataframe, on='uniprotID', how='left')
323
  data.positions = data.positions.astype('str')
 
324
  for i in data.index:
325
  if (str(data.at[i, 'pos']) in data.at[i, 'positions']) and data.at[i, 'trsh4'] == 'surface':
326
  data.at[i, 'threeState_trsh4_HQ'] = 'interface'
 
459
  minutes, seconds = divmod(rem, 60)
460
  print("Time passed: {:0>2}:{:0>2}:{:05.2f}".format(int(hours), int(minutes), seconds))
461
  #sys.stdout.close()
462
+ return data
463
+
464
+