我想从一堆PDB文件中提取特定链的单字母氨基酸序列。
我能够使用SeqIO.parse()来做到这一点,但我认为这很不合常规:
PDB_file_path = '/full/path/to/some/pdb'
# Is there a 1-liner for this ?
query_seqres = SeqIO.parse(PDB_file_path, 'pdb-seqres')
for chain in query_seqres:
if chain.id == query_chain_id:
query_chain = chain.seq
#
是否有更简洁明了的方法?
我认为这不是Pythonic,但您可以执行以下操作:
from Bio import SeqIO
PDB_file_path = '6q62.pdb'
query_chain_id = '6Q62:A'
chain = {record.id: record.seq for record in SeqIO.parse(PDB_file_path, 'pdb-seqres')}
query_chain = chain[query_chain_id]