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Update Renum_chain.py for Biopython 2.0 #2

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Update Renum_chain.py for Biopython 2.0 #2

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5 changes: 3 additions & 2 deletions server_bin/Renum_chain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
from Bio.PDB.PDBIO import PDBIO
from Bio import PDB, SeqIO,AlignIO
from Bio.Align import PairwiseAligner
from Bio.Data.PDBData import protein_letters_3to1

def get_args():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
Expand Down Expand Up @@ -73,7 +74,7 @@ def get_sequence_from_model(structure):
for chain in structure:
for residue in chain:
if PDB.is_aa(residue,standard=True):
seq_data += PDB.Polypeptide.three_to_one(residue.get_resname())
seq_data += protein_letters_3to1[residue.get_resname()]
resnum_tbl.append(residue.id[1])
return seq_data,resnum_tbl

Expand Down Expand Up @@ -190,4 +191,4 @@ def main():
io.save(OutPath)

if __name__ == '__main__':
main()
main()