Bio.PDB.mmcifio module
Write an mmCIF file.
See https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax for syntax.
- class Bio.PDB.mmcifio.MMCIFIO
Bases:
StructureIO
Write a Structure object or a mmCIF dictionary as a mmCIF file.
Examples
>>> from Bio.PDB import MMCIFParser >>> from Bio.PDB.mmcifio import MMCIFIO >>> parser = MMCIFParser() >>> structure = parser.get_structure("1a8o", "PDB/1A8O.cif") >>> io=MMCIFIO() >>> io.set_structure(structure) >>> io.save("bio-pdb-mmcifio-out.cif") >>> import os >>> os.remove("bio-pdb-mmcifio-out.cif") # tidy up
- __init__()
Initialise.
- set_dict(dic)
Set the mmCIF dictionary to be written out.
- save(filepath, select=_select, preserve_atom_numbering=False)
Save the structure to a file.
- Parameters:
filepath (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.