From 0157853bda109c824299009a08ade96276138664 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 17 Feb 2025 22:58:34 +0100
Subject: [PATCH] update Ubuntu/Debian install docs
---
modules/doc/install.rst | 45 ++++++++++++++++++++++++++++++++---------
1 file changed, 36 insertions(+), 9 deletions(-)
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index 42cf59b91..0060a81b4 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -310,27 +310,28 @@ observed for OpenMM versions 6.1 until 7.1.1 when compiling with gcc versions >=
from source.
-**Ubuntu 20.04 LTS / Debian 10 with GUI**
+**Ubuntu 24.04 LTS**
+Besides the molecular mechanics module, we also enable parasail here.
All the dependencies can be installed from the package manager as follows:
.. code-block:: bash
sudo apt-get install cmake g++ libtiff-dev libfftw3-dev libeigen3-dev \
libpng-dev python3-all python3-pyqt5 libboost-all-dev \
- qt5-qmake qtbase5-dev libpng-dev libsqlite3-dev
+ qt5-qmake qtbase5-dev libpng-dev libsqlite3-dev \
+ libopenmm-dev libopenmm-plugins libparasail-dev
Now, all dependencies are located in standard locations and cmake will
-automatically find them without the need to pass any additional parameters.
-We add -DOPTIMIZE, which will tell cmake to build an optimised version of
-OpenStructure.
+automatically find them. As a single quirk, we need to specify the
+OpenMM plugin directory. Lets do a proper out of source build here:
.. code-block:: bash
- cmake . -DOPTIMIZE=ON
-
-
-
+ mkdir build
+ cd build
+ cmake .. -DOPTIMIZE=ON -DENABLE_MM=1 -DENABLE_PARASAIL=1 \
+ -DOPEN_MM_PLUGIN_DIR=/lib/x86_64-linux-gnu/openmm/plugins
**macOS (Catalina/ Big Sur/ Monterey) with Homebrew**
@@ -413,6 +414,26 @@ to run multiple jobs at once.
What's next?
--------------------------------------------------------------------------------
+One thing is missing for a fully functional OpenStructure installation.
+The compound library. It is used at various places for connectivity
+information and certain algorithms do not work without.
+Besides an OpenStructure executable, we just built the
+chemdict_tool which converts the PDB chemical component dictionary
+into our internal format:
+
+.. code-block:: bash
+
+ wget https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
+ stage/bin/chemdict_tool create components.cif.gz <compounds.chemlib>
+
+We can rerun cmake and make. All cmake parameters from the original
+configuration remain in the cache.
+
+.. code-block:: bash
+
+ cmake .. -DCOMPOUND_LIB=<compounds.chemlib>
+ make
+
On Linux and macOS, you can start dng from the command-line. The binaries are
all located in stage/bin:
@@ -426,6 +447,12 @@ or, to start the command-line interpreter:
stage/bin/ost
+But hey, good citizen run the unit tests first:
+
+.. code-block:: bash
+
+ make check
+
If you repeatedly use OpenStructure, it is recommended to add
/path/to/ost/stage/bin to your path.
--
GitLab