myenv/lib/python3.10/site-packages/Bio/SeqIO/PdbIO.py

# Copyright 2012 by Eric Talevich.  All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for accessing sequences in PDB and mmCIF files."""
import collections
import warnings

from Bio import BiopythonParserWarning
from Bio.Data.PDBData import protein_letters_3to1
from Bio.Data.PDBData import protein_letters_3to1_extended
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

from .Interfaces import SequenceIterator


_aa3to1_dict = {}
_aa3to1_dict.update(protein_letters_3to1)
_aa3to1_dict.update(protein_letters_3to1_extended)


def _res2aacode(residue, undef_code="X"):
    """Return the one-letter amino acid code from the residue name.

    Non-amino acid are returned as "X".
    """
    if isinstance(residue, str):
        return _aa3to1_dict.get(residue, undef_code)

    return _aa3to1_dict.get(residue.resname, undef_code)


def AtomIterator(pdb_id, structure):
    """Return SeqRecords from Structure objects.

    Base function for sequence parsers that read structures Bio.PDB parsers.

    Once a parser from Bio.PDB has been used to load a structure into a
    Bio.PDB.Structure.Structure object, there is no difference in how the
    sequence parser interprets the residue sequence. The functions in this
    module may be used by SeqIO modules wishing to parse sequences from lists
    of residues.

    Calling functions must pass a Bio.PDB.Structure.Structure object.


    See Bio.SeqIO.PdbIO.PdbAtomIterator and Bio.SeqIO.PdbIO.CifAtomIterator for
    details.
    """
    model = structure[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 _res2aacode(res.get_resname().upper()) != "X"
        ]
        if not residues:
            continue
        # 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 and rnumbers[i + 1] != rnum:
                # 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(_res2aacode(x) for x in residues[prev_idx:i])
                    prev_idx = i
                    res_out.append("X" * gapsize)
                else:
                    warnings.warn(
                        "Ignoring out-of-order residues after a gap",
                        BiopythonParserWarning,
                    )
                    # Keep the normal part, drop the out-of-order segment
                    # (presumably modified or hetatm residues, e.g. 3BEG)
                    res_out.extend(_res2aacode(x) for x in residues[prev_idx:i])
                    break
            else:
                # Last segment
                res_out.extend(_res2aacode(x) for x in residues[prev_idx:])
        else:
            # No gaps
            res_out = [_res2aacode(x) for x in residues]
        record_id = f"{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)), id=record_id, description=record_id)
        # TODO: Test PDB files with DNA and RNA too:
        record.annotations["molecule_type"] = "protein"

        record.annotations["model"] = model.id
        record.annotations["chain"] = chain.id

        record.annotations["start"] = int(rnumbers[0])
        record.annotations["end"] = int(rnumbers[-1])
        yield record


class PdbSeqresIterator(SequenceIterator):
    """Parser for PDB files."""

    def __init__(self, source):
        """Return SeqRecord objects for each chain in a PDB file.

        Arguments:
         - source - input stream opened in text mode, or a path to a 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, DBREF1, DBREF2, SEQADV, SEQRES, MODRES

        See: http://www.wwpdb.org/documentation/format23/sect3.html

        This gets called internally via Bio.SeqIO for the SEQRES based interpretation
        of the PDB file format:

        >>> from Bio import SeqIO
        >>> for record in SeqIO.parse("PDB/1A8O.pdb", "pdb-seqres"):
        ...     print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
        ...     print(record.dbxrefs)
        ...
        Record id 1A8O:A, chain A
        ['UNP:P12497', 'UNP:POL_HV1N5']

        Equivalently,

        >>> with open("PDB/1A8O.pdb") as handle:
        ...     for record in PdbSeqresIterator(handle):
        ...         print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
        ...         print(record.dbxrefs)
        ...
        Record id 1A8O:A, chain A
        ['UNP:P12497', 'UNP:POL_HV1N5']

        Note the chain is recorded in the annotations dictionary, and any PDB DBREF
        lines are recorded in the database cross-references list.
        """
        super().__init__(source, mode="t", fmt="PDB")

    def parse(self, handle):
        """Start parsing the file, and return a SeqRecord generator."""
        records = self.iterate(handle)
        return records

    def iterate(self, handle):
        """Iterate over the records in the PDB file."""
        chains = collections.defaultdict(list)
        metadata = collections.defaultdict(list)

        rec_name = None
        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 = [_res2aacode(res) 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,
                    }
                )
            elif rec_name == "DBREF1":
                # ID code of this entry (PDB ID)
                pdb_id = line[7:11]
                # Chain identifier.
                chn_id = line[12]
                # Sequence database name.
                database = line[26:32].strip()
                # Sequence database identification code.
                db_id_code = line[47:67].strip()
            elif rec_name == "DBREF2":
                # Ensure ID code and chain are consistent:
                if pdb_id != line[7:11] or chn_id != line[12]:
                    raise ValueError("DBREF2 identifiers do not match")
                # Sequence database accession code.
                db_acc = line[18:40].strip()
                metadata[chn_id].append(
                    {
                        "pdb_id": pdb_id,
                        "database": database,
                        "db_acc": db_acc,
                        "db_id_code": db_id_code,
                    }
                )
            # ENH: 'SEQADV' 'MODRES'

        if rec_name is None:
            raise ValueError("Empty file.")

        for chn_id, residues in sorted(chains.items()):
            record = SeqRecord(Seq("".join(residues)))
            record.annotations = {"chain": chn_id}
            # TODO: Test PDB files with DNA and RNA too:
            record.annotations["molecule_type"] = "protein"
            if chn_id in metadata:
                m = metadata[chn_id][0]
                record.id = record.name = f"{m['pdb_id']}:{chn_id}"
                record.description = f"{m['database']}:{m['db_acc']} {m['db_id_code']}"
                for melem in metadata[chn_id]:
                    record.dbxrefs.extend(
                        [
                            f"{melem['database']}:{melem['db_acc']}",
                            f"{melem['database']}:{melem['db_id_code']}",
                        ]
                    )
            else:
                record.id = chn_id
            yield record


def PdbAtomIterator(source):
    """Return SeqRecord objects for each chain in a PDB file.

    Argument source is a file-like object or a path to a 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
    annotation:

    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.

    This gets called internally via Bio.SeqIO for the atom based interpretation
    of the PDB file format:

    >>> from Bio import SeqIO
    >>> for record in SeqIO.parse("PDB/1A8O.pdb", "pdb-atom"):
    ...     print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
    ...
    Record id 1A8O:A, chain A

    Equivalently,

    >>> with open("PDB/1A8O.pdb") as handle:
    ...     for record in PdbAtomIterator(handle):
    ...         print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
    ...
    Record id 1A8O:A, chain A

    """
    # TODO - Add record.annotations to the doctest, esp the residues (not working?)

    # Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
    from Bio.PDB import PDBParser

    structure = PDBParser().get_structure(None, source)
    pdb_id = structure.header["idcode"]
    if not pdb_id:
        warnings.warn(
            "'HEADER' line not found; can't determine PDB ID.", BiopythonParserWarning
        )
        pdb_id = "????"

    for record in AtomIterator(pdb_id, structure):
        # The PDB header was loaded as a dictionary, so let's reuse it all
        record.annotations.update(structure.header)

        # ENH - add letter annotations -- per-residue info, e.g. numbers

        yield record


PDBX_POLY_SEQ_SCHEME_FIELDS = (
    "_pdbx_poly_seq_scheme.asym_id",  # Chain ID
    "_pdbx_poly_seq_scheme.mon_id",  # Residue type
)

STRUCT_REF_FIELDS = (
    "_struct_ref.id",  # ID of this reference
    "_struct_ref.db_name",  # Name of the database
    "_struct_ref.db_code",  # Code for this entity
    "_struct_ref.pdbx_db_accession",  # DB accession ID of ref
)

STRUCT_REF_SEQ_FIELDS = (
    "_struct_ref_seq.ref_id",  # Pointer to _struct_ref
    "_struct_ref_seq.pdbx_PDB_id_code",  # PDB ID of this structure
    "_struct_ref_seq.pdbx_strand_id",  # Chain ID of the reference
)


def CifSeqresIterator(source):
    """Return SeqRecord objects for each chain in an mmCIF file.

    Argument source is a file-like object or a path to a file.

    The sequences are derived from the _entity_poly_seq entries in the mmCIF
    file, not the atoms of the 3D structure.

    Specifically, these mmCIF records are handled: _pdbx_poly_seq_scheme and
    _struct_ref_seq. The _pdbx_poly_seq records contain sequence information,
    and the _struct_ref_seq records contain database cross-references.

    See:
    http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/pdbx_poly_seq_scheme.html
    and
    http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/struct_ref_seq.html

    This gets called internally via Bio.SeqIO for the sequence-based
    interpretation of the mmCIF file format:

    >>> from Bio import SeqIO
    >>> for record in SeqIO.parse("PDB/1A8O.cif", "cif-seqres"):
    ...     print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
    ...     print(record.dbxrefs)
    ...
    Record id 1A8O:A, chain A
    ['UNP:P12497', 'UNP:POL_HV1N5']

    Equivalently,

    >>> with open("PDB/1A8O.cif") as handle:
    ...     for record in CifSeqresIterator(handle):
    ...         print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
    ...         print(record.dbxrefs)
    ...
    Record id 1A8O:A, chain A
    ['UNP:P12497', 'UNP:POL_HV1N5']

    Note the chain is recorded in the annotations dictionary, and any mmCIF
    _struct_ref_seq entries are recorded in the database cross-references list.
    """
    # Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
    from Bio.PDB.MMCIF2Dict import MMCIF2Dict

    chains = collections.defaultdict(list)
    metadata = collections.defaultdict(list)
    records = MMCIF2Dict(source)

    # Explicitly convert records to list (See #1533).
    # If an item is not present, use an empty list
    for field in (
        PDBX_POLY_SEQ_SCHEME_FIELDS + STRUCT_REF_SEQ_FIELDS + STRUCT_REF_FIELDS
    ):
        if field not in records:
            records[field] = []
        elif not isinstance(records[field], list):
            records[field] = [records[field]]

    for asym_id, mon_id in zip(
        records["_pdbx_poly_seq_scheme.asym_id"],
        records["_pdbx_poly_seq_scheme.mon_id"],
    ):
        mon_id_1l = _res2aacode(mon_id)
        chains[asym_id].append(mon_id_1l)

    # Build a dict of _struct_ref records, indexed by the id field:
    struct_refs = {}
    for ref_id, db_name, db_code, db_acc in zip(
        records["_struct_ref.id"],
        records["_struct_ref.db_name"],
        records["_struct_ref.db_code"],
        records["_struct_ref.pdbx_db_accession"],
    ):
        struct_refs[ref_id] = {
            "database": db_name,
            "db_id_code": db_code,
            "db_acc": db_acc,
        }

    # Look through _struct_ref_seq records, look up the corresponding
    # _struct_ref and add an entry to the metadata list for this chain.
    for ref_id, pdb_id, chain_id in zip(
        records["_struct_ref_seq.ref_id"],
        records["_struct_ref_seq.pdbx_PDB_id_code"],
        records["_struct_ref_seq.pdbx_strand_id"],
    ):
        struct_ref = struct_refs[ref_id]

        # The names here mirror those in PdbIO
        metadata[chain_id].append({"pdb_id": pdb_id})
        metadata[chain_id][-1].update(struct_ref)

    for chn_id, residues in sorted(chains.items()):
        record = SeqRecord(Seq("".join(residues)))
        record.annotations = {"chain": chn_id}
        # TODO: Test PDB files with DNA and RNA too:
        record.annotations["molecule_type"] = "protein"
        if chn_id in metadata:
            m = metadata[chn_id][0]
            record.id = record.name = f"{m['pdb_id']}:{chn_id}"
            record.description = f"{m['database']}:{m['db_acc']} {m['db_id_code']}"
            for melem in metadata[chn_id]:
                record.dbxrefs.extend(
                    [
                        f"{melem['database']}:{melem['db_acc']}",
                        f"{melem['database']}:{melem['db_id_code']}",
                    ]
                )
        else:
            record.id = chn_id
        yield record


def CifAtomIterator(source):
    """Return SeqRecord objects for each chain in an mmCIF file.

    Argument source is a file-like object or a path to a file.

    The sequences are derived from the 3D structure (_atom_site.* fields)
    in the mmCIF file.

    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
    annotation:

    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.

    This gets called internally via Bio.SeqIO for the atom based interpretation
    of the PDB file format:

    >>> from Bio import SeqIO
    >>> for record in SeqIO.parse("PDB/1A8O.cif", "cif-atom"):
    ...     print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
    ...
    Record id 1A8O:A, chain A

    Equivalently,

    >>> with open("PDB/1A8O.cif") as handle:
    ...     for record in CifAtomIterator(handle):
    ...         print("Record id %s, chain %s" % (record.id, record.annotations["chain"]))
    ...
    Record id 1A8O:A, chain A

    """
    # TODO - Add record.annotations to the doctest, esp the residues (not working?)

    # Only import parser when needed, to avoid/delay NumPy dependency in SeqIO
    from Bio.PDB.MMCIFParser import MMCIFParser

    structure = MMCIFParser().get_structure(None, source)
    pdb_id = structure.header["idcode"]
    if not pdb_id:
        warnings.warn("Could not determine the PDB ID.", BiopythonParserWarning)
        pdb_id = "????"
    yield from AtomIterator(pdb_id, structure)


if __name__ == "__main__":
    from Bio._utils import run_doctest

    run_doctest(verbose=0)