Bio.PDB.mmcifio module¶
Write an mmCIF file.
See https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax for syntax.
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class
Bio.PDB.mmcifio.
MMCIFIO
¶ Bases:
Bio.PDB.PDBIO.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
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__init__
(self)¶ Initialise.
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set_dict
(self, dic)¶ Set the mmCIF dictionary to be written out.
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save
(self, filepath, select=<Select all>, 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.
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