From de707c8da2723ce2390915ce2e141c458dae15b5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 16 Sep 2021 19:15:12 +0200
Subject: [PATCH] OMF documentation
---
modules/io/doc/io.rst | 87 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 87 insertions(+)
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 381771ad9..b64a01e79 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -95,6 +95,93 @@ behaviour.
pdb_str = pdb.read()
ent = io.PDBStrToEntity(pdb_str, ost.io.profiles['DEFAULT'], True)
+
+.. class:: ost.io.OMF
+
+ Experimental data format capable of storing minimally required information
+ of a :class:`ost.mol.EntityHandle` in a heavily compressed manner
+ (OMF - OpenStructure Minimal Format). Shares lots of ideas with the mmtf or
+ binaryCIF formats but comes with no dependencies attached.
+
+ .. staticmethod:: FromEntity(ent)
+
+ Generates :class:`ost.io.OMF` object starting from an
+ :class:`ost.mol.EntityHandle`. *ent* is is assigned as assymetric unit,
+ no biounits are defined (i.e. :func:`GetBU` raises an error in any case`).
+
+ :param ent: Structural data
+ :type ent: :class:`ost.mol.EntityHandle`
+ :returns: The created :class:`ost.io.OMF` object
+
+ .. staticmethod:: FromFile(filepath)
+
+ Generates :class:`ost.io.OMF` object from a file stored with
+ :func:`ToFile`.
+
+ :param filepath: The file
+ :type filepath: :class:`str`
+ :returns: The created :class:`ost.io.OMF` object
+
+ .. staticmethod:: FromMMCIF(ent, info)
+
+ Generates :class:`ost.io.OMF` object starting from an
+ :class:`ost.mol.EntityHandle` with an associated :class:`MMCifInfo`
+ (you get this stuff with :func:`ost.io.LoadMMCIF`). *ent* is assigned
+ as assymetric unit and the biounits are fetched from *info*.
+
+ :param ent: Structural data
+ :type ent: :class:`ost.mol.EntityHandle`
+ :param info: Biounits are fetched from here
+ :type info: :class:`MMCifInfo`
+ :returns: The created :class:`ost.io.OMF` object
+
+ .. staticmethod:: FromBytes(bytes_string)
+
+ Generates :class:`ost.io.OMF` object from a :class:`bytes` object created
+ with :func:`ToBytes`.
+
+ :param bytes_string: The super heavily compressed OMF structure
+ :type bytes_string: :class:`bytes`
+
+ .. method:: ToFile(filepath)
+
+ Stores object to file
+
+ :param filepath: The file
+ :type filepath: :class:`str`
+
+ .. method:: ToBytes()
+
+ Stores object to :class:`bytes` string
+
+ :returns: The :class:`bytes` string
+
+ .. method:: GetAU()
+
+ Getter for assymetric unit
+
+ :returns: The assymetric unit as :class:`ost.mol.EntityHandle`
+
+ .. method:: GetAUChain(chain_name)
+
+ Getter for single chain in the assymetric unit
+
+ :param chain_name: The name of the chain you want
+ :type chain_name: :class:`str`
+ :returns: :class:`ost.mol.EntityHandle` of the AU only containing the
+ specified chain
+
+ .. method:: GetBU(bu_idx)
+
+ Getter for Biounit
+
+ :param bu_idx: The index from the biounit as it has been read from *info* in
+ :func:`FromMMCIF`.
+ :type bu_idx: :class:`int`
+ :returns: The Biounit as :class:`ost.mol.EntityHandle`
+ :raises: :class:`RuntimeError` if *bu_idx* doesn't exist
+
+
Loading Molecular Structures From Remote Repositories
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
--
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