def _get_pdb_sequence(structure):
"""
Retrieves the AA sequence from a PDB structure.
"""
_aainfo = lambda r: (r.id[1], aa3to1.get(r.resname, 'X'))
seq = map(_aainfo, structure.get_residues())
return seq
def get_pdb_sequence(structure):
"""
Retrieves the AA sequence from a PDB structure.
"""
_aainfo = lambda r: (r.id[1], aa3to1.get(r.resname, 'X'))
seq = [_aainfo(r) for r in structure.get_residues() if is_aa(r)]
return seq
def get_pdb_sequence_with_chains(structure):
"""
Retrieves the AA sequence from a PDB structure. It's a list that looks like [(5, 'R', 'A'), (6, 'E', 'A'), (7, 'H', 'A'), (8, 'W', 'A'),...]
"""
_aainfo = lambda r: (r.id[1], aa3to1.get(r.resname, 'X'),r.get_parent().get_id(),r.id[0],r.id[2])
seq = [_aainfo(r) for r in structure.get_residues() if (is_aa(r) and r.has_id('CA'))]
return seq
def _get_pdb_sequence(structure):
"""
Retrieves the AA sequence from a PDB structure.
"""
_aainfo = lambda r: (r.id[1], aa3to1.get(r.resname, 'X'))
seq = map(_aainfo, structure.get_residues())
return seq
def get_pdb_sequence(structure):
"""
Retrieves the AA sequence from a PDB structure.
"""
aa = lambda r: (r.id[1], prot_one_letter.get(r.resname, 'X'))
seq = []
for r in structure.get_residues():
if Bio.PDB.Polypeptide.is_aa(r):
seq.append(aa(r))
return seq
def get_sequence(self, chain_id):
'''
Input:
self: Use Biopython.PDB structure which has been stored in an object variable
chain_id : String (usually in ['A','B', 'C' ...]. The number of chains
depends on the specific protein and the resulting structure)
Return:
Return the amino acid sequence (single-letter alphabet!) of a given chain (chain_id)
in a Biopython.PDB structure as a string.
'''
for model in self.structure:
if chain_id in model:
chain = model[chain_id]
sequence = ""
for residue in chain.get_list():
nom = aa3to1.get(residue.get_resname())
if nom != None:
sequence += nom
return sequence