Doc update - properly link mmCIF parts.

modules/io/doc/io.rst

@@ -61,12 +61,11 @@ on the file extension.
       :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
       inexistent file.
 
-Some of the formats have a dedicated function that allows you to tweak many 
-parameters that affect the import. PDB files can be loaded with 
-:func:`~ost.io.LoadPDB`. It offers tighter control over the exact loading behaviour.
-
-
-:doc:`profile`
+Some of the formats have a dedicated function that allows you to tweak many
+parameters that affect the import. PDB files can be loaded with  :func:`LoadPDB`
+and mmCIF files with :func:`LoadMMCIF` (this also gives you access to the
+:class:`MMCifInfo` class). It offers tighter control over the exact loading
+behaviour.
 
 
 .. autofunction:: ost.io.LoadPDB

modules/io/doc/mmcif.rst

 mmCIF File Format
 --------------------------------------------------------------------------------
 
+.. currentmodule:: ost.io
+
 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 (:class:`MMCifInfo`,
 :class:`MMCifInfoCitation`, :class:`MMCifInfoTransOp`,
-:class:`MMCifInfoBioUnit`, :class:`MMCifInfoStructDetails`).
+:class:`MMCifInfoBioUnit`, :class:`MMCifInfoStructDetails`,
+:class:`MMCifInfoObsolete`, :class:`MMCifInfoStructRef`,
+:class:`MMCifInfoStructRefSeq`, :class:`MMCifInfoStructRefSeqDif`,
+:class:`MMCifInfoRevisions`).
 
 
 Loading mmCIF Files
@@ -20,8 +25,8 @@ Categories Available
 The following categories of a mmCIF file are considered by the reader:
 
 * ``atom_site``: Used to build the :class:`~ost.mol.EntityHandle`
-* ``entity``: Involved in setting ChainTypes
-* ``entity_poly``: Involved in setting ChainTypes
+* ``entity``: Involved in setting :class:`~ost.mol.ChainType` of chains
+* ``entity_poly``: Involved in setting :class:`~ost.mol.ChainType` of chains
 * ``citation``: Goes into :class:`MMCifInfoCitation`
 * ``citation_author``: Goes into :class:`MMCifInfoCitation`
 * ``exptl``: Goes into :class:`MMCifInfo` as :attr:`~MMCifInfo.method`.
@@ -39,7 +44,7 @@ The following categories of a mmCIF file are considered by the reader:
 * ``pdbx_database_PDB_obs_spr``: Verbose information on obsoleted/ superseded
   entries, stored in :class:`MMCifInfoObsolete`
 * ``struct_ref`` stored in :class:`MMCifInfoStructRef`
-* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeq`
+* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeqDif`
 * ``struct_ref_seq_dif`` stored in :class:`MMCifInfoStructRefDif`
 * ``database_pdb_rev`` (mmCIF dictionary version < 5) stored in
   :class:`MMCifInfoRevisions`

modules/io/doc/structure_formats.rst

 Supported Structure File Formats
 ================================================================================
 
-The following file formats are supported by :func:`~ost.io.LoadEntity`:
+.. currentmodule:: ost.io
 
+The following file formats are supported by :func:`LoadEntity`:
 
 
 CRD - CARD format file used by CHARMM
@@ -14,9 +15,9 @@ This trajectory file format is used by the CHARMM program suite (Molecular Model
 
 PDB - Brookhaven PDB File
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Fine grained control over PDB file import is available via the 
-:func:`~ost.io.LoadPDB` function. The PDB importer supports loading gzipped PDB 
-files, which are auto-detected by the .gz file extension.
+Fine grained control over PDB file import is available via the :func:`LoadPDB`
+function. The PDB importer supports loading gzipped PDB files, which are auto-
+detected by the .gz file extension.
 
 *Recognized File Extensions*
   .ent, .pdb, .ent.gz, .pdb.gz
@@ -26,10 +27,10 @@ files, which are auto-detected by the .gz file extension.
 
 mmCIF - macromolecular Crystallographic Information File
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Fine grained control over mmCIFile import is available via the 
-:func:`~ost.io.LoadMMCIF` function. Most notably, this gives you access to the
-:class:`MMCifInfo` class. The mmCIF importer supports loading gzipped files,
-which are auto-detected by the .gz file extension.
+Fine grained control over mmCIFile import is available via the :func:`LoadMMCIF`
+function. Most notably, this gives you access to the :class:`MMCifInfo` class.
+The mmCIF importer supports loading gzipped files, which are auto-detected by
+the .gz file extension.
 
 *Recognized File Extensions*
   .cif, .cif.gz