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3ab87a2
1
Parent(s):
8337c15
Update code/pdb_featureVector.py
Browse files
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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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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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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