# Copyright 2012 by Eric Talevich.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
import collections
import warnings
from Bio.Alphabet import generic_protein
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Data.SCOPData import protein_letters_3to1
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.SeqUtils
    from Bio.SeqUtils import seq1
    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 = [seq1(res, custom_map=protein_letters_3to1) for res in line[19:].split()]
        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.items()):
        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'],
            for melem in metadata[chn_id]:
                    "%s:%s" % (melem['database'], melem['db_acc']),
                    "%s:%s" % (melem['database'], melem['db_id_code'])])
            record.id = chn_id
        yield record
def PdbAtomIterator(handle):
    """Returns SeqRecord objects for each chain in a PDB file
    The sequences are derived from the 3D structure (ATOM records), not the
    SEQRES lines in the PDB file header.
    Unrecognised three letter amino acid codes (e.g. "CSD") from HETATM entries
    are converted to "X" in the sequence.
    In addition to information from the PDB header (which is the same for all
    records), the following chain specific information is placed in the
    record.annotations["residues"] = List of residue ID strings
    record.annotations["chain"] = Chain ID (typically A, B ,...)
    record.annotations["model"] = Model ID (typically zero)
    Where amino acids are missing from the structure, as indicated by residue
    numbering, the sequence is filled in with 'X' characters to match the size
    of the missing region, and  None is included as the corresponding entry in
    the list record.annotations["residues"].
    This function uses the Bio.PDB module to do most of the hard work. The
    annotation information could be improved but this extra parsing should be
    done in parse_pdb_header, not this module.
    # Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
    from Bio.PDB import PDBParser
    from Bio.SeqUtils import seq1
    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 seq1(residue.resname, custom_map=protein_letters_3to1)
    # Deduce the PDB ID from the PDB header
    # ENH: or filename?
    from Bio.File import UndoHandle
    undo_handle = UndoHandle(handle)
    firstline = undo_handle.peekline()
    if firstline.startswith("HEADER"):
        pdb_id = firstline[62:66]
        warnings.warn("First line is not a 'HEADER'; can't determine PDB ID")
        pdb_id = '????'
    struct = PDBParser().get_structure(pdb_id, undo_handle)
    model = struct[0]
    for chn_id, chain in sorted(model.child_dict.items()):
        # HETATM mod. res. policy: remove mod if in sequence, else discard
        residues = [res for res in chain.get_unpacked_list()
                    if seq1(res.get_resname().upper(),
                        custom_map=protein_letters_3to1) != "X"]
        if not residues:
        # Identify missing residues in the structure
        # (fill the sequence with 'X' residues in these regions)
        gaps = []
        rnumbers = [r.id[1] for r in residues]
        for i, rnum in enumerate(rnumbers[:-1]):
            if rnumbers[i+1] != rnum + 1:
                # It's a gap!
                gaps.append((i+1, rnum, rnumbers[i+1]))
        if gaps:
            res_out = []
            prev_idx = 0
            for i, pregap, postgap in gaps:
                if postgap > pregap:
                    gapsize = postgap - pregap - 1
                    res_out.extend(restype(x) for x in  residues[prev_idx:i])
                    prev_idx = i
                    warnings.warn("Ignoring out-of-order residues after a gap",
                    # Keep the normal part, drop the out-of-order segment
                    # (presumably modified or hetatm residues, e.g. 3BEG)
                    res_out.extend(restype(x) for x in residues[prev_idx:i])
                # Last segment
                res_out.extend(restype(x) for x in residues[prev_idx:])
            # No gaps
            res_out = [restype(x) for x in residues]
        record_id = "%s:%s" % (pdb_id, chn_id)
        # ENH - model number in SeqRecord id if multiple models?
        # id = "Chain%s" % str(chain.id)
        # if len(structure) > 1 :
        #     id = ("Model%s|" % str(model.id)) + id
        record = SeqRecord(Seq(''.join(res_out), generic_protein),
        # The PDB header was loaded as a dictionary, so let's reuse it all
        record.annotations = struct.header.copy()
        # Plus some chain specifics:
        record.annotations["model"] = model.id
        record.annotations["chain"] = chain.id
        # Start & end
        record.annotations["start"] = int(rnumbers[0])
        record.annotations["end"] = int(rnumbers[-1])
        # ENH - add letter annotations -- per-residue info, e.g. numbers
        yield record
if __name__ == '__main__':
    # Test
    import sys
    from Bio import SeqIO
    for fname in sys.argv[1:]:
        for parser in (PdbSeqresIterator, PdbAtomIterator):
            with open(fname) as handle:
                records = parser(handle)
                SeqIO.write(records, sys.stdout, 'fasta')