# Bio.PDB.PDBIO module

Output of PDB files.

class Bio.PDB.PDBIO.Select

  Bases: `object`

  Select everything for PDB output (for use as a base class).

  Default selection (everything) during writing - can be used as base class to implement selective output. This selects which entities will be written out.

  __repr__()

    Represent the output as a string for debugging.

  accept_model(model)

    Overload this to reject models for output.

  accept_chain(chain)

    Overload this to reject chains for output.

  accept_residue(residue)

    Overload this to reject residues for output.

  accept_atom(atom)

    Overload this to reject atoms for output.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 62
  __static_attributes__ = ()

class Bio.PDB.PDBIO.StructureIO

  Bases: `object`

  Base class to derive structure file format writers from.

  __init__()

    Initialise.

  set_structure(pdb_object)

    Check what the user is providing and build a structure.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 93
  __static_attributes__ = ('structure',)

class Bio.PDB.PDBIO.PDBIO(use_model_flag=0, is_pqr=False)

  Bases: `StructureIO`

  Write a Structure object (or a subset of a Structure object) as a PDB or PQR file.

  Examples

      >>> from Bio.PDB import PDBParser
      >>> from Bio.PDB.PDBIO import PDBIO
      >>> parser = PDBParser()
      >>> structure = parser.get_structure("1a8o", "PDB/1A8O.pdb")
      >>> io=PDBIO()
      >>> io.set_structure(structure)
      >>> io.save("bio-pdb-pdbio-out.pdb")
      >>> import os
      >>> os.remove("bio-pdb-pdbio-out.pdb")  # tidy up

  __init__(use_model_flag=0, is_pqr=False)

    Create the PDBIO object.

    Parameters:

      - use_model_flag (int) – if 1, force use of the MODEL record in output.

      - is_pqr (Boolean) – if True, build PQR file. Otherwise build PDB file.

  save(file, select=_select, write_end=True, preserve_atom_numbering=False)

    Save structure to a file.

    Parameters:

      - file (string or filehandle) – output file

      - select (object) – selects which entities will be written.

    Typically select is a subclass of L{Select}, it should have the following methods:

    > - accept_model(model)

    > - accept_chain(chain)

    > - accept_residue(residue)

    > - accept_atom(atom)

    These methods should return 1 if the entity is to be written out, 0 otherwise.

    Typically select is a subclass of L{Select}.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 150
  __static_attributes__ = ('is_pqr', 'use_model_flag')

Biopython v: 1.86

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