fatmacankara commited on
Commit
3ab87a2
·
1 Parent(s): 8337c15

Update code/pdb_featureVector.py

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Files changed (1) hide show
  1. code/pdb_featureVector.py +8 -1
code/pdb_featureVector.py CHANGED
@@ -1379,21 +1379,28 @@ def pdb(input_set, mode, impute):
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  data['pdbSequence'] = data['pdbSequence'].str.replace('U', 'C')
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  st.write('HERE')
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  for i in data.index:
 
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  id_ = data.at[i, 'pdbID'].lower()
 
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  up_id_ = data.at[i, 'uniprotID']
 
 
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  score_ = str(data.at[i, 'score'])
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-
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  if data.at[i, 'source'] == 'PDB':
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  pdb_path = Path(path_to_output_files / 'pdb_structures' / f'{id_}.pdb')
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  elif data.at[i, 'source'] == 'MODBASE':
 
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  pdb_path = Path(path_to_output_files / 'modbase_structures_individual' / f'{id_}.txt')
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  elif data.at[i, 'source'] == 'SWISSMODEL':
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  pdb_path = Path(path_to_output_files / 'swissmodel_structures' / f'{up_id_}_{id_}_{score_}.txt')
 
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  pdbSequence = data.at[i, 'pdbSequence']
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  source = data.at[i, 'source']
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  chain = data.at[i, 'chain']
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  uniprotID = data.at[i, 'uniprotID']
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  pdbID = data.at[i, 'pdbID']
 
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  alignments = get_alignments_3D(uniprotID, 'nan', pdb_path, pdbSequence, source, chain, pdbID, mode, Path(path_to_output_files / '3D_alignment'), file_format = 'gzip')
 
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  data['pdbSequence'] = data['pdbSequence'].str.replace('U', 'C')
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  st.write('HERE')
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  for i in data.index:
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+ st.write('i', i)
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  id_ = data.at[i, 'pdbID'].lower()
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+ st.write('id_', id_)
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  up_id_ = data.at[i, 'uniprotID']
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+ st.write('up_id_', up_id_)
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+
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  score_ = str(data.at[i, 'score'])
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+ st.write('score_', score_)
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  if data.at[i, 'source'] == 'PDB':
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  pdb_path = Path(path_to_output_files / 'pdb_structures' / f'{id_}.pdb')
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  elif data.at[i, 'source'] == 'MODBASE':
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+ st.write('Hewew2')
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  pdb_path = Path(path_to_output_files / 'modbase_structures_individual' / f'{id_}.txt')
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  elif data.at[i, 'source'] == 'SWISSMODEL':
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  pdb_path = Path(path_to_output_files / 'swissmodel_structures' / f'{up_id_}_{id_}_{score_}.txt')
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+
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  pdbSequence = data.at[i, 'pdbSequence']
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  source = data.at[i, 'source']
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  chain = data.at[i, 'chain']
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  uniprotID = data.at[i, 'uniprotID']
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  pdbID = data.at[i, 'pdbID']
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+
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  alignments = get_alignments_3D(uniprotID, 'nan', pdb_path, pdbSequence, source, chain, pdbID, mode, Path(path_to_output_files / '3D_alignment'), file_format = 'gzip')