scripts/pdb/xpdb.py

# Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0

"""
PDB parsers for large files with Biopython.
Modified from https://biopython.org/wiki/Reading_large_PDB_files
"""

import sys
import Bio.PDB
import Bio.PDB.StructureBuilder
from Bio.PDB.Residue import Residue


class SloppyStructureBuilder(Bio.PDB.StructureBuilder.StructureBuilder):
    """Cope with resSeq < 10,000 limitation by just incrementing internally."""

    def __init__(self, verbose=False):
        Bio.PDB.StructureBuilder.StructureBuilder.__init__(self)
        self.max_resseq = -1
        self.verbose = verbose

    def init_residue(self, resname, field, resseq, icode):
        """Initiate a new Residue object.

        Arguments:
            resname: string, e.g. "ASN"
            field: hetero flag, "W" for waters, "H" for hetero residues, otherwise blanc.
            resseq: int, sequence identifier
            icode: string, insertion code

        Return:
            None
        """
        if field != " ":
            if field == "H":
                # The hetero field consists of
                # H_ + the residue name (e.g. H_FUC)
                field = "H_" + resname
        res_id = (field, resseq, icode)

        if resseq > self.max_resseq:
            self.max_resseq = resseq

        if field == " ":
            fudged_resseq = False
            while self.chain.has_id(res_id) or resseq == 0:
                # There already is a residue with the id (field, resseq, icode)
                # resseq == 0 catches already wrapped residue numbers which
                # do not trigger the has_id() test.
                #
                # Be sloppy and just increment...
                # (This code will not leave gaps in resids... I think)
                #
                # XXX: shouldn't we also do this for hetero atoms and water??
                self.max_resseq += 1
                resseq = self.max_resseq
                res_id = (field, resseq, icode)  # use max_resseq!
                fudged_resseq = True

            if fudged_resseq and self.verbose:
                sys.stderr.write(
                    "Residues are wrapping (Residue "
                    + "('%s', %i, '%s') at line %i)."
                    % (field, resseq, icode, self.line_counter)
                    + ".... assigning new resid %d.\n" % self.max_resseq
                )
        residue = Residue(res_id, resname, self.segid)
        self.chain.add(residue)
        self.residue = residue
        return None


class SloppyPDBIO(Bio.PDB.PDBIO):
    """PDBIO class that can deal with large pdb files as used in MD simulations

    - resSeq simply wrap and are printed modulo 10,000.
    - atom numbers wrap at 99,999 and are printed modulo 100,000

    """

    # The format string is derived from the PDB format as used in PDBIO.py
    # (has to be copied to the class because of the package layout it is not
    # externally accessible)
    _ATOM_FORMAT_STRING = (
        "%s%5i %-4s%c%3s %c%4i%c   "
        + "%8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n"
    )

    def _get_atom_line(
        self,
        atom,
        hetfield,
        segid,
        atom_number,
        resname,
        resseq,
        icode,
        chain_id,
        element="  ",
        charge="  ",
    ):
        """Returns an ATOM string that is guaranteed to fit the ATOM format.

        - Resid (resseq) is wrapped (modulo 10,000) to fit into %4i (4I) format
        - Atom number (atom_number) is wrapped (modulo 100,000) to fit into
          %5i (5I) format

        Args: #TODO
            atom:
            hetfield:
            segid:
            atom_number:
            resname:
            resseq:
            icode:
            chain_id:
            element:
            charge:

        Returns:
            #TODO
        """
        if hetfield != " ":
            record_type = "HETATM"
        else:
            record_type = "ATOM  "
        name = atom.get_fullname()
        altloc = atom.get_altloc()
        x, y, z = atom.get_coord()
        bfactor = atom.get_bfactor()
        occupancy = atom.get_occupancy()
        args = (
            record_type,
            atom_number % 100000,
            name,
            altloc,
            resname,
            chain_id,
            resseq % 10000,
            icode,
            x,
            y,
            z,
            occupancy,
            bfactor,
            segid,
            element,
            charge,
        )
        return self._ATOM_FORMAT_STRING % args