Bio.PDB.PDBIO module¶
Output of PDB files.
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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.
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__repr__
(self)¶ Represent the output as a string for debugging.
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accept_model
(self, model)¶ Overload this to reject models for output.
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accept_chain
(self, chain)¶ Overload this to reject chains for output.
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accept_residue
(self, residue)¶ Overload this to reject residues for output.
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accept_atom
(self, atom)¶ Overload this to reject atoms for output.
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class
Bio.PDB.PDBIO.
StructureIO
¶ Bases:
object
Base class to derive structure file format writers from.
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__init__
(self)¶ Initialise.
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set_structure
(self, pdb_object)¶ Check what the user is providing and build a structure.
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class
Bio.PDB.PDBIO.
PDBIO
(use_model_flag=0, is_pqr=False)¶ Bases:
Bio.PDB.PDBIO.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
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__init__
(self, 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.
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save
(self, file, select=<Select all>, 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}.
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