def PdbSeqresIterator(handle):
"""Returns SeqRecord objects for each chain in a PDB file.
The sequences are derived from the SEQRES lines in the
PDB file header, not the atoms of the 3D structure.
Specifically, these PDB records are handled: DBREF, SEQADV, SEQRES, MODRES
See: http://www.wwpdb.org/documentation/format23/sect3.html
"""
# Late-binding import to avoid circular dependency on SeqIO in Bio.SCOP
# TODO - swap in Bow's SeqUtils.seq1 once that's merged
from Bio.SCOP.three_to_one_dict import to_one_letter_code
chains = collections.defaultdict(list)
metadata = collections.defaultdict(list)
for line in handle:
rec_name = line[0:6].strip()
if rec_name == 'SEQRES':
# NB: We only actually need chain ID and the residues here;
# commented bits are placeholders from the wwPDB spec.
# Serial number of the SEQRES record for the current chain.
# Starts at 1 and increments by one each line.
# Reset to 1 for each chain.
# ser_num = int(line[8:10])
# Chain identifier. This may be any single legal character,
# including a blank which is used if there is only one chain.
chn_id = line[11]
# Number of residues in the chain (repeated on every record)
# num_res = int(line[13:17])
residues = [to_one_letter_code.get(res, 'X')
for res in line[19:].split()]
chains[chn_id].extend(residues)
elif rec_name == 'DBREF':
# ID code of this entry (PDB ID)
pdb_id = line[7:11]
# Chain identifier.
chn_id = line[12]
# Initial sequence number of the PDB sequence segment.
# seq_begin = int(line[14:18])
# Initial insertion code of the PDB sequence segment.
# icode_begin = line[18]
# Ending sequence number of the PDB sequence segment.
# seq_end = int(line[20:24])
# Ending insertion code of the PDB sequence segment.
# icode_end = line[24]
# Sequence database name.
database = line[26:32].strip()
# Sequence database accession code.
db_acc = line[33:41].strip()
# Sequence database identification code.
db_id_code = line[42:54].strip()
# Initial sequence number of the database seqment.
# db_seq_begin = int(line[55:60])
# Insertion code of initial residue of the segment, if PDB is the
# reference.
# db_icode_begin = line[60]
# Ending sequence number of the database segment.
# db_seq_end = int(line[62:67])
# Insertion code of the ending residue of the segment, if PDB is the
# reference.
# db_icode_end = line[67]
metadata[chn_id].append({'pdb_id': pdb_id, 'database': database,
'db_acc': db_acc, 'db_id_code': db_id_code})
# ENH: 'SEQADV' 'MODRES'
for chn_id, residues in sorted(chains.iteritems()):
record = SeqRecord(Seq(''.join(residues), generic_protein))
record.annotations = {"chain": chn_id}
if chn_id in metadata:
m = metadata[chn_id][0]
record.id = record.name = "%s:%s" % (m['pdb_id'], chn_id)
record.description = ("%s:%s %s" % (m['database'],
m['db_acc'],
m['db_id_code']))
for melem in metadata[chn_id]:
record.dbxrefs.extend([
"%s:%s" % (melem['database'], melem['db_acc']),
"%s:%s" % (melem['database'], melem['db_id_code'])])
else:
record.id = chn_id
yield record
def PdbSeqresIterator(handle):
"""Returns SeqRecord objects for each chain in a PDB file.
The sequences are derived from the SEQRES lines in the
PDB file header, not the atoms of the 3D structure.
Specifically, these PDB records are handled: DBREF, SEQADV, SEQRES, MODRES
See: http://www.wwpdb.org/documentation/format23/sect3.html
"""
# Late-binding import to avoid circular dependency on SeqIO in Bio.SCOP
# TODO - swap in Bow's SeqUtils.seq1 once that's merged
from Bio.SCOP.three_to_one_dict import to_one_letter_code
chains = collections.defaultdict(list)
metadata = collections.defaultdict(list)
for line in handle:
rec_name = line[0:6].strip()
if rec_name == 'SEQRES':
# NB: We only actually need chain ID and the residues here;
# commented bits are placeholders from the wwPDB spec.
# Serial number of the SEQRES record for the current chain.
# Starts at 1 and increments by one each line.
# Reset to 1 for each chain.
# ser_num = int(line[8:10])
# Chain identifier. This may be any single legal character,
# including a blank which is used if there is only one chain.
chn_id = line[11]
# Number of residues in the chain (repeated on every record)
# num_res = int(line[13:17])
residues = [to_one_letter_code.get(res, 'X')
for res in line[19:].split()]
chains[chn_id].extend(residues)
elif rec_name == 'DBREF':
# ID code of this entry (PDB ID)
pdb_id = line[7:11]
# Chain identifier.
chn_id = line[12]
# Initial sequence number of the PDB sequence segment.
# seq_begin = int(line[14:18])
# Initial insertion code of the PDB sequence segment.
# icode_begin = line[18]
# Ending sequence number of the PDB sequence segment.
# seq_end = int(line[20:24])
# Ending insertion code of the PDB sequence segment.
# icode_end = line[24]
# Sequence database name.
database = line[26:32].strip()
# Sequence database accession code.
db_acc = line[33:41].strip()
# Sequence database identification code.
db_id_code = line[42:54].strip()
# Initial sequence number of the database seqment.
# db_seq_begin = int(line[55:60])
# Insertion code of initial residue of the segment, if PDB is the
# reference.
# db_icode_begin = line[60]
# Ending sequence number of the database segment.
# db_seq_end = int(line[62:67])
# Insertion code of the ending residue of the segment, if PDB is the
# reference.
# db_icode_end = line[67]
metadata[chn_id].append({'pdb_id': pdb_id, 'database': database,
'db_acc': db_acc, 'db_id_code': db_id_code})
# ENH: 'SEQADV' 'MODRES'
for chn_id, residues in sorted(chains.iteritems()):
record = SeqRecord(Seq(''.join(residues), generic_protein))
record.annotations = {"chain": chn_id}
if chn_id in metadata:
m = metadata[chn_id][0]
record.id = record.name = "%s:%s" % (m['pdb_id'], chn_id)
record.description = ("%s:%s %s" % (m['database'],
m['db_acc'],
m['db_id_code']))
for melem in metadata[chn_id]:
record.dbxrefs.extend([
"%s:%s" % (melem['database'], melem['db_acc']),
"%s:%s" % (melem['database'], melem['db_id_code'])])
else:
record.id = chn_id
yield record
def restype(residue):
"""Return a residue's type as a one-letter code.
Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
"""
return to_one_letter_code.get(residue.resname, 'X')
