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Update code/alphafold_featureVector.py
Browse files- code/alphafold_featureVector.py +16 -28
code/alphafold_featureVector.py
CHANGED
@@ -587,9 +587,9 @@ def alphafold(input_set, mode, impute):
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pdb_path = hf_hub_download(repo_id="HuBioDataLab/AlphafoldStructures", filename=f"AF-{uniprotID}-F{mod}-model_v4.pdb.gz",repo_type = 'dataset')
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with gzip.open(pdb_path, mode="rt") as f:
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st.write('Download complete.')
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@@ -611,31 +611,19 @@ def alphafold(input_set, mode, impute):
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atomSequence = ''
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coords = []
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resnums_for_sasa = []
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st.write('Hello I am in 3Dalignment GZIP')
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with gzip.open(pdb_path, mode='rb') as f:
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for line in f:
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line = line.decode()
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if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
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atomSequence += threeToOne(line[17:20].strip())
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coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
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resnums_for_sasa.append(line[22:26].strip())
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elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
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atomSequence += threeToOne(line[17:20].strip())
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coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
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resnums_for_sasa.append(line[22:26].strip())
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#f = open(Path(path_3D_alignment / f'{identifier}_{str(model_num)}_3Dalignment.txt'),"w")
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aligner.mode = 'local'
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aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
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pdb_path = hf_hub_download(repo_id="HuBioDataLab/AlphafoldStructures", filename=f"AF-{uniprotID}-F{mod}-model_v4.pdb.gz",repo_type = 'dataset')
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#with gzip.open(pdb_path, mode="rt") as f:
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# file_content = f.read()
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# st.write(file_content)
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st.write('Download complete.')
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atomSequence = ''
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coords = []
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resnums_for_sasa = []
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st.write('Hello I am in 3Dalignment GZIP')
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with gzip.open(pdb_path, mode='rb') as f:
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for line in f:
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line = line.decode()
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if line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA':
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atomSequence += threeToOne(line[17:20].strip())
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coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
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resnums_for_sasa.append(line[22:26].strip())
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elif line[0:4].strip() == 'ATOM' and line[13:15].strip() == 'CA' and line[21] == ' ':
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atomSequence += threeToOne(line[17:20].strip())
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coords.append([line[31:38].strip(), line[39:46].strip(), line[47:54].strip()])
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resnums_for_sasa.append(line[22:26].strip())
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st.write('o-complee')
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#f = open(Path(path_3D_alignment / f'{identifier}_{str(model_num)}_3Dalignment.txt'),"w")
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aligner.mode = 'local'
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aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
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