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e7fe90a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | #!/usr/bin/env python3
"""
extract_chain_seq.py
Extracts the 1-letter amino acid sequence for a specified chain
from a PDB or mmCIF file.
Usage:
python extract_chain_seq.py <input_file> <chain_id>
Outputs:
The amino acid sequence on stdout (no header).
"""
import sys
import gemmi
from Bio.PDB import PDBParser
# --- Robust import for three_to_one across Biopython versions ---
try:
from Bio.PDB.Polypeptide import three_to_one
except ImportError:
try:
from Bio.SeqUtils import seq1 as three_to_one
except ImportError:
from Bio.PDB.Polypeptide import protein_letters_3to1
def three_to_one(resname):
resname = (resname or "").strip().upper()
if resname == "MSE":
resname = "MET"
return protein_letters_3to1.get(resname.title(), "X")
if len(sys.argv) != 3:
print("Usage: python extract_chain_seq.py <input_file> <chain_id>")
sys.exit(1)
path = sys.argv[1]
chain_id = sys.argv[2]
ext = path.lower().split(".")[-1]
def seq_from_pdb(pdb_path, chain):
parser = PDBParser(QUIET=True)
try:
structure = parser.get_structure("x", pdb_path)
except Exception as e:
sys.stderr.write(f"Error reading PDB: {e}\n")
return ""
for model in structure:
for c in model:
if c.id == chain:
seq = ""
for res in c:
try:
seq += three_to_one(res.get_resname())
except KeyError:
pass
return seq
return ""
def seq_from_cif(cif_path, chain):
try:
doc = gemmi.cif.read_file(cif_path)
structure = gemmi.make_structure_from_block(doc.sole_block())
except Exception as e:
sys.stderr.write(f"Error reading CIF: {e}\n")
return ""
for model in structure:
for c in model:
if c.name == chain:
seq = ""
for res in c:
if res.is_amino_acid():
seq += gemmi.residue_name_3to1.get(res.name, "")
return seq
return ""
# Select correct parser
if ext == "pdb":
seq = seq_from_pdb(path, chain_id)
elif ext in ("cif", "mmcif", "mcif"):
seq = seq_from_cif(path, chain_id)
else:
sys.stderr.write(f"Unsupported file extension: {ext}\n")
seq = ""
# Output sequence
print(seq)
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