Package Bio :: Package PDB :: Module PDBIO' :: Class PDBIO

Class PDBIO

object --+
         |
        PDBIO

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

Example:

>>> p=PDBParser()
>>> s=p.get_structure("1fat", "1fat.pdb")
>>> io=PDBIO()
>>> io.set_structure(s)
>>> io.save("out.pdb")

Instance Methods

[hide private]

__init__(self, use_model_flag=0)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

_get_atom_line(self, atom, hetfield, segid, atom_number, resname, resseq, icode, chain_id, charge=' ')
Returns an ATOM PDB string (PRIVATE). source code

save(self, file, select=<Select all>, write_end=0)

source code

set_structure(self, structure)

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, use_model_flag=0)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

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

Overrides: object.__init__

save(self, file, select=<Select all>, write_end=0)

source code

Parameters:

file (string or filehandle) - output file
select (select hould 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 Select.
) - selects which entities will be written.

Class PDBIO

__init__(self, use_model_flag=0) (Constructor)

save(self, file, select=<Select all>, write_end=0)

init(self, use_model_flag=0)
(Constructor)