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# 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
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