From cdc42d20bb6dc4bf8a4a515105c0ce0fcf4cc1ae Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 21 Sep 2017 12:00:20 +0200
Subject: [PATCH] Doc update - properly link mmCIF parts.
---
modules/io/doc/io.rst | 11 +++++------
modules/io/doc/mmcif.rst | 13 +++++++++----
modules/io/doc/structure_formats.rst | 17 +++++++++--------
3 files changed, 23 insertions(+), 18 deletions(-)
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 3dbc2ac6e..f8f5302e0 100644
--- a/modules/io/doc/io.rst
+++ b/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
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 0098cd503..730ca1b8e 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -1,11 +1,16 @@
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`
diff --git a/modules/io/doc/structure_formats.rst b/modules/io/doc/structure_formats.rst
index ce9c8aedd..a80133842 100644
--- a/modules/io/doc/structure_formats.rst
+++ b/modules/io/doc/structure_formats.rst
@@ -1,8 +1,9 @@
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
--
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