mmCIF File Format
The mmCIF file format is an alternate container for structural entities, also provided by the PDB. Here we describe how to load those files and how to deal with information provided above the common PDB format.
Loading mmCIF Files
Categories Available
The following categories of a mmCIF file are considered by the parser:
-
atom_site: Used to build the :class:`entity <ost.mol.EntityHandle>` -
entity: Involved in setting ChainTypes -
entity_poly: Involved in setting ChainTypes -
citation: Goes into :class:`MMCifInfoCitation` -
citation_author: Goes into :class:`MMCifInfoCitation` -
exptl: Goes into :class:`MMCifInfo` as :attr:`method <MMCifInfo.method>`. -
refine: Goes into :class:`MMCifInfo` as :attr:`resolution <MMCifInfo.resolution>`. -
pdbx_struct_assembly: Used for :class:`MMCifInfoBioUnit`. -
pdbx_struct_assembly_gen: Used for :class:`MMCifInfoBioUnit`. -
pdbx_struct_oper_list: Used for :class:`MMCifInfoBioUnit`. -
struct: Details about a structure, stored in :class:`MMCifInfoStructDetails`.
Info Classes
Information from mmCIF files which goes beyond structural data, is kept in a special container, the :class:`MMCifInfo` class. Here is a detailed description of the annotation available.
This is the container for all bits of non-molecular data pulled from a mmCIF file.
This stores citation information from an input file.
This stores operations needed to transform an :class:`entity <ost.mol.EntityHandle>` into a biounit.
This stores information how a structure is to be assembled to form the biounit.
Holds details about the structure.