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schwede
openstructure
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d3fee7ec
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d3fee7ec
authored
13 years ago
by
Bienchen
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Added documentation about the categories parsed by the mmCIF parser.
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modules/io/doc/mmcif.rst
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modules/io/doc/mmcif.rst
modules/io/src/mol/mmcif_reader.hh
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modules/io/src/mol/mmcif_reader.hh
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modules/io/doc/mmcif.rst
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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
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modules/io/src/mol/mmcif_reader.hh
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@@ -45,6 +45,9 @@ namespace ost { namespace io {
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@@ -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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