From 9262ea8f7cbb24b8322d3c57676d0c01701375c2 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Wed, 5 Jul 2017 19:59:07 +0200
Subject: [PATCH] SCHWED-1786: documented functions for default compounds
library
---
modules/conop/doc/compoundlib.rst | 26 ++++++++++++++++++--------
modules/doc/install.rst | 5 ++++-
2 files changed, 22 insertions(+), 9 deletions(-)
diff --git a/modules/conop/doc/compoundlib.rst b/modules/conop/doc/compoundlib.rst
index bf1450036..f88f04709 100644
--- a/modules/conop/doc/compoundlib.rst
+++ b/modules/conop/doc/compoundlib.rst
@@ -19,6 +19,20 @@ latest compound definitions, follow :ref:`these instructions <mmcif-convert>` to
build the compound library manually.
+.. function:: GetDefaultLib()
+
+ :return: Default compound library set by :func:`SetDefaultLib`. If you got
+ OpenStructure as a bundle or you :ref:`compiled <cmake-flags>` it
+ with a specified ``COMPOUND_LIB`` flag, this will return a compound
+ library when executing scripts with ``ost``.
+ :rtype: :class:`CompoundLib`
+
+.. function:: SetDefaultLib(lib)
+
+ :param lib: Library to be set as default compound library.
+ :type lib: :class:`CompoundLib`
+
+
.. class:: CompoundLib
.. staticmethod:: Load(database, readonly=True)
@@ -69,19 +83,15 @@ build the compound library manually.
.. method:: GetOSTVersionUsed()
- reads out ost_version_used from the table chemlib_info.
-
- :returns: a version string
-
- :rtype: :class:`String`
+ :return: OST version (ost_version_used from the table chemlib_info)
+ :rtype: :class:`str`
.. method:: GetCreationDate()
- reads out creation_date from the table chemlib_info.
+ :return: creation date (creation_date from the table chemlib_info)
+ :rtype: :class:`str`
- :returns: a date string (Py), a Date (C++)
- :rtype: :class:`String` (Py), :class:`Date`
.. class:: Compound
Holds the description of a chemical compound, such as three-letter-code, and
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 759d7392f..e4970bb54 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -118,6 +118,8 @@ On Windows you have to explicitly set the build generator to "Visual Studio 9 20
cmake -G"Visual Studio 9 2008"
+.. _cmake-flags:
+
Flags to Control the Dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -141,7 +143,8 @@ By default, `CMake <http://cmake.org>`_ searches the standard directories for de
of a certain residue or connectivities between atoms etc. The
:doc:`compound library <conop/compoundlib>` itself is created from the
component dictionary by calling the OpenStructure chemdict_tool.
- By default this is switched off.
+ By default this is switched off but it is highly recommended to provide a
+ compound library to use all features of OpenStructure.
* `COMPILE_TMTOOLS` will activate bindings for TMAlign and TMScore, which are
then available at python level. This option requires a Fortran compiler.
--
GitLab