How can I get the length of a protein chain from a PDB file with Biopython? - biopython

Question

I have tried it this way first:
for model in structure:
for residue in model.get_residues():
if PDB.is_aa(residue):
x += 1
and then that way:
len(structure[0][chain])
But none of them seem to work...

Answer 1

Your code should work and give you the correct results.
from Bio import PDB
parser = PDB.PDBParser()
pdb1 ='./1bfg.pdb'
structure = parser.get_structure("1bfg", pdb1)
model = structure[0]
res_no = 0
non_resi = 0
for model in structure:
for chain in model:
for r in chain.get_residues():
if r.id[0] == ' ':
res_no +=1
else:
non_resi +=1
print ("Residues: %i" % (res_no))
print ("Other: %i" % (non_resi))
res_no2 = 0
non_resi2 = 0
for model in structure:
for residue in model.get_residues():
if PDB.is_aa(residue):
res_no2 += 1
else:
non_resi2 += 1
print ("Residues2: %i" % (res_no2))
print ("Other2: %i" % (non_resi2))
Output:
Residues: 126
Other: 99
Residues2: 126
Other2: 99
Your statement
print (len(structure[0]['A']))
gives you the sum (225) of all residues, in this case all amino acids and water atoms.
The numbers seem to be correct when compared to manual inspection using PyMol.
What is the specific error message you are getting or the output you are expecting? Any specific PDB file?
Since the PDB file is mostly used to store the coordinates of the resolved atoms, it is not always possible to get the full structure. Another approach would be use to the cif files.
from Bio import PDB
parser = PDB.PDBParser()
pdb1 ='./1bfg.cif'
m = PDB.MMCIF2Dict.MMCIF2Dict(pdb1)
if '_entity_poly.pdbx_seq_one_letter_code' in m.keys():
print ('Full structure:')
full_structure = (m['_entity_poly.pdbx_seq_one_letter_code'])
print (full_structure)
print (len(full_structure))
Output:
Full structure:
PALPEDGGSGAFPPGHFKDPKRLYCKNGGFFLRIHPDGRVDGVREKSDPHIKLQLQAEERGVVSIKGVSANRYLAMKEDGRLLASKSVTDECFFFERLESNNYNTYRSRKYTSWYVALKRTGQYKLGSKTGPGQKAILFLPMSAKS
146
For multiple chains:
from Bio import PDB
parser = PDB.PDBParser()
pdb1 ='./4hlu.cif'
m = PDB.MMCIF2Dict.MMCIF2Dict(pdb1)
if '_entity_poly.pdbx_seq_one_letter_code' in m.keys():
full_structure = m['_entity_poly.pdbx_seq_one_letter_code']
chains = m['_entity_poly.pdbx_strand_id']
for c in chains:
print('Chain %s' % (c))
print('Sequence: %s' % (full_structure[chains.index(c)]))

Answer 2

It's just:
from Bio.PDB import PDBParser
from Bio import PDB
pdb = PDBParser().get_structure("1bfg", "1bfg.pdb")
for chain in pdb.get_chains():
print(len([_ for _ in chain.get_residues() if PDB.is_aa(_)]))

Answer 3

I appreciated Peters' answer, but I also realized the res.id[0] == " " is more robust (i.e. HIE). PDB.is_aa() cannot detect HIE is an amino acid while HIE is ε-nitrogen protonated histidine. So I recommend:
from Bio import PDB
parser = PDB.PDBParser()
pdb1 ='./1bfg.pdb'
structure = parser.get_structure("1bfg", pdb)
model = structure[0]
res_no = 0
non_resi = 0
for model in structure:
for chain in model:
for r in chain.get_residues():
if r.id[0] == ' ':
res_no +=1
else:
non_resi +=1
print ("Residues: %i" % (res_no))
print ("Other: %i" % (non_resi))

Answer 4

I think you would actually want to do something like
m = Bio.PDB.MMCIF2Dict.MMCIF2Dict(pdb_cif_file)
if '_entity_poly.pdbx_seq_one_letter_code' in m.keys():
full_structure = m['_entity_poly.pdbx_seq_one_letter_code']
chains = m['_entity_poly.pdbx_strand_id']
for c in chains:
for ci in c.split(','):
print('Chain %s' % (ci))
print('Sequence: %s' % (full_structure[chains.index(c)]))