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Commit d3fee7ec authored by Bienchen's avatar Bienchen
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Added documentation about the categories parsed by the mmCIF parser.

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MMCif File Format mmCIF File Format
-------------------------------------------------------------------------------- --------------------------------------------------------------------------------
The MMCif file format is an alternate container for structural entities, also 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 provided by the PDB. Here we describe how to load those files and how to deal
with information provided above the common PDB format. with information provided above the common PDB format.
Loading MMCif Files Loading mmCIF Files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autofunction:: ost.io.LoadMMCIF .. autofunction:: ost.io.LoadMMCIF
...@@ -15,17 +15,31 @@ Loading MMCif Files ...@@ -15,17 +15,31 @@ Loading MMCif Files
Categories Available 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`.
Info Classes Info Classes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Information from MMCif files which goes beyond structural data, is kept in a Information from mmCIF files which goes beyond structural data, is kept in a
special container, the :class:`MMCifInfo` class. Here is a detailed description special container, the :class:`MMCifInfo` class. Here is a detailed description
of the annotation available. of the annotation available.
.. class:: MMCifInfo .. class:: MMCifInfo
This is the container for all bits of non-molecular data pulled from a MMCif This is the container for all bits of non-molecular data pulled from a mmCIF
file. file.
.. attribute:: citations .. attribute:: citations
......
...@@ -45,6 +45,9 @@ namespace ost { namespace io { ...@@ -45,6 +45,9 @@ namespace ost { namespace io {
/// \li entity /// \li entity
/// \li entity_poly /// \li entity_poly
/// \li citation /// \li citation
/// \li citation_author
/// \li exptl
/// \li refine
/// \li pdbx_struct_assembly /// \li pdbx_struct_assembly
/// \li pdbx_struct_assembly_gen /// \li pdbx_struct_assembly_gen
/// \li pdbx_struct_oper_list /// \li pdbx_struct_oper_list
......
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