You are reading the documentation for version 2.3.1 of OpenStructure. You may also want to read the documentation for: 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.7.1 1.8 1.9 1.10 1.11 2.0 2.1 2.2 2.3 devel

Installing OpenStructure From Source¶

Brief Overview¶

For a simple and portable way to use OpenStructure we recommend using a container solution. We provide recipes to build images for Docker and Singularity. The latest recipes and instructions can be found on our GitLab site, including a link to OpenStructure’s own GitLab Docker registry (Docker instructions and Singularity instructions).

If you wish to compile OpenStructure outside of a container, you need to follow the steps which we describe in detail below. In essence, these steps are:

• Installing the Dependencies
• Checking out the source code from GIT
• Configuring the build with cmake

Installing the Dependencies¶

OpenStructure requires a C++11 enabled compiler (e.g. recent gcc/clang) and uses a bunch of open-source libraries. If you haven’t already installed them, please install them now! Where appropriate, the minimally required version is given in parentheses.

• CMake (3.12.1)
• Python3 (3.6)
• Boost (1.68)
• zlib (usually comes with Boost or system)
• Eigen3 (3.3.1)
• SQLite3 (3.24.0)
• FFTW3. By default, OpenStructure is compiled with single precision and thus also requires FFTW to be compiled with single precision. Most platforms offer this as a second package. If you are compiling manually, use the –enable-single option.
• libtiff
• libpng (also needed for GUI)

If you would like to use the info module, also install:

If you would like to use the graphical user interface (GUI), also install:

If you would like to use the molecular mechanics module:

We do not provide backwards compatibility to Python 2.7. The last release supporting Python 2.7 is 1.11.0.

Getting the Source Code¶

OpenStructure uses git as the revision control system. The main repository can be browsed here. To get the source code, use git clone:

git clone https://git.scicore.unibas.ch/schwede/openstructure.git <directory-name>


The above command will clone OpenStructure into the directory specified by <directory-name>. If omitted, the directory will be called openstructure.

Note

Some versions of curl have trouble with the certificate of the OpenStructure git server and fail to clone the repository. To work around this, disable the SSL certificate verification by setting the following environment variable:

export GIT_SSL_NO_VERIFY=1


Picking the right branch¶

By default you are checking out the master branch. Master is by definition a stable branch. It always points to the latest release. However, there are several other branches at your disposal. The main development is happening in the develop branch. It contains the newest features and bug fixes. However, we don’t make any guarantees that the develop branch is bug free and doesn’t contain major bugs. After all, it’s in constant flux. If you are developing new features, start your feature branch off develop. Besides that, there are several smaller features branches that are used to group together commits for one specific features. To change to a specific branch, use

git checkout <branch-name>


Configuring¶

OpenStructure uses CMake for compiling and building the project. The next required step is to configure the build environment using cmake. You can do that by invoking cmake in the project directory.

cmake . <options>


There are two kinds of options: Options that let you control the building behaviour, enabling and disabling the compilation of certain modules and options that let you tell CMake where to find the dependencies. All of them are passed to CMake via -D<opt>=<value>.

Flag to choose build generator¶

CMake supports different build generators. On UNIX, i.e. macOS and Linux, the default build generator is Makefiles, but it is also possible to use other programs. For a list of supported build generators on your platform, run cmake without parameters.

Flags to Control the Dependencies¶

By default, CMake searches the standard directories for dependencies. However, on some systems, this might not be enough. Here is a short description of how CMake figures out what dependencies to take and how you can influence it.

• Boost is mainly controlled via the BOOST_ROOT option. If boost wasn’t found, it should be set to the prefix of the boost installation. If for some reason, it is desirable to use the non-multithreaded boost libraries, you can switch Boost_USE_MULTITHREADED off (it is on by default).
• Python_ROOT_DIR is the Python equivalent of BOOST_ROOT. It should be set to the prefix path containing the python binary, headers and libraries.
• SYS_ROOT controls the general prefix for searching libraries and headers. By default, it is set to /.
• COMPOUND_LIB specifies the location of the compound library and activates the rule-based-builder. The compound library is based on the component dictionary released by the PDB, and it specifies atoms of a certain residue or connectivities between atoms etc. The compound library itself is created from the component dictionary by calling the OpenStructure chemdict_tool. By default this is switched off but it is highly recommended to provide a compound library to use all features of OpenStructure.
• ENABLE_GUI controls whether to build the graphical user interface module. By default, this is switched on.
• ENABLE_GFX controls whether to build the graphics module. By default, this is switched on. If it is switched off, it also switches ENABLE_GUI off.
• ENABLE_INFO controls whether to build the info module. By default, this is switched on. If it is switched off, it also switches ENABLE_GFX off and removes all dependencies to Qt.
• QT_QMAKE_EXECUTABLE defines the exact Qt installation to take. It should be set to the full path to qmake. This is only needed if ENABLE_INFO is switched on.
• COMPILE_TMTOOLS will activate bindings for TMAlign and TMScore, which are then available at python level. This option requires a Fortran compiler. By default, this option is switched off.
• USE_NUMPY allows OpenStructure to pass back data in NumPy format. By default, this is switched off.
• ENABLE_MM controls whether the molecular mechanics module is enabled. By default, this is switched off. If it is turned on, you should also set the paths to your local OpenMM installation:
• OPEN_MM_INCLUDE_DIR: the include path
• OPEN_MM_LIBRARY: the libOpenMM library
• OPEN_MM_PLUGIN_DIR: the path for OpenMM plugins
• see example below for commonly used paths
• Several paths to other libraries can be set if they are not in the expected locations:
• Python_LIBRARY defines the location of the Python library (file name starting with libpython). This must be set if it is not in $Python_ROOT_DIR/lib. • EIGEN3_INCLUDE_DIR defines the include folder of Eigen3 (contains Eigen folder with include files). • FFTW_LIBRARY defines the location of the FFTW3 library (file name starting with libfftw3f (or libfftw3 if USE_DOUBLE_PRECISION is switched on)) • FFTW_INCLUDE_DIR defines the include folder of FFTW3 (contains include files directly) • PNG_LIBRARY defines the location of the libpng library (file name starting with libpng) • PNG_PNG_INCLUDE_DIR defines the include folder of libpng (contains include files directly) • ZLIB_LIBRARY defines the location of the zlib library (file name starting with libz) • ZLIB_INCLUDE_DIR defines the include folder of zlib (contains include files directly) • TIFF_LIBRARY defines the location of the libtiff library (file name starting with libtiff) • TIFF_INCLUDE_DIR defines the include folder of libtiff (contains include files directly) • SQLITE3_LIBRARY defines the location of the SQLite3 library (file name starting with libsqlite3) • SQLITE3_INCLUDE_DIR defines the include folder of SQLite3 (contains include files directly) • Usually, you will receive errors for those variables when executing cmake and set them accordingly as needed. • OPENGLPREFERENCE_LEGACY switches the GL implementation to be used by OpenGL. The default is what should be used on modern systems. But since there are some reports on the internet claiming that the default does not work everywhere, this switch enables the usage of the legacy implementation of GL. Build Options¶ • OPTIMIZE can be switched on to build an optimised (-O3 -DNDEBUG) version of OpenStructure. By default, this is switched off. • USE_DOUBLE_PRECISION will switch on double precision within OpenStructure. By default, this is switched off. • ENABLE_STATIC allows some parts of OpenStructure to be statically linked and thus can be used more easily across a heterogeneous setup, e.g. older systems and newer systems. Note that enabling this flag will not compile the full OpenStructure package and it is not guaranteed to lead to fully portable binaries. By default, this is switched off. • For deployment of OpenStructure with make install there are two relevant settings to consider: • PREFIX or CMAKE_INSTALL_PREFIX are used to define the path where the OpenStructure stage folder will be installed to. • USE_RPATH can be switched on to embed rpath upon make install. By default, this option is switched off. • Experimental settings (only change if you know what you are doing): • USE_SHADER controls whether to compile with shader support. By default, this is turned off. • ENABLE_SPNAV controls whether 3DConnexion devices should be supported. By default, this is turned off. • PROFILE can be switched on to enable a (very verbose) code profiler. By default, this is turned off. • UBUNTU_LAYOUT can be turned on to switch the directory layout of the stage folder to be more ubuntu-like. By default, this is switched off. • HIDDEN_VISIBILITY can be turned on to add “-fvisibility=hidden” to gcc’s compile flags (only if GNU compiler used). By default, this is switched off. Known Issues¶ • Depending on how the dependecies (e.g. Boost) are compiled, linking might fail with something like: error: undefined reference to pthread_condattr_destroy. Add “-pthread” to the linking options by appending the following to your cmake command: -DCMAKE_EXE_LINKER_FLAGS=” -pthread” Example Configurations¶ Generic Linux without GUI The simplest way to compile OpenStructure is to disable the GUI and any dependency to Qt5. You can build an optimised OpenStructure without GUI as follows: cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF  The molecular mechanics module can be enabled by installing OpenMM and adding the appropriate flags as follows (replace <OPENMM> with the actual path to OpenMM): cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF -DENABLE_MM=ON \ -DOPEN_MM_LIBRARY=<OPENMM>/lib/libOpenMM.so \ -DOPEN_MM_INCLUDE_DIR=<OPENMM>/include/ \ -DOPEN_MM_PLUGIN_DIR=<OPENMM>/lib/plugins  Note that the OpenMM binaries available online may be incompatible with files compiled using your gcc compiler (known as “Dual ABI” issue). This has been observed for OpenMM versions 6.1 until 7.1.1 when compiling with gcc versions >= 5.1. In those cases, you cannot use the binaries and will have to install OpenMM from source. Ubuntu 20.04 LTS / Debian 10 with GUI All the dependencies can be installed from the package manager as follows: 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  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. cmake . -DOPTIMIZE=ON  macOS (Catalina/ Big Sur/ Monterey) with Homebrew Note When switching the Qt version used for compiling OST with support for the graphical user interface, dng may start behaving weird. Symptoms are that the user interface starts being unresponsive to mouse clicks. An easy solution may be to close dng and remove $HOME/Library/Preferences/org.openstructure.dng.plist and start dng again.

Homebrew can be used to conveniently install all dependencies. The current Python version, as of writing these instructions, is 3.9.10 but works so far. Boost comes as 1.76.0 which seems to be OK. Do not forget to also install boost-python3 (your system may have a lower version of Python than 3.9.10 but it seems like boost-python3 was compiled for 3.9.10). Eigen and SQLite also seem to be unproblematic concerning higher version numbers. To build the graphical user interface, use Qt version 5 by installing packages qt@5 and pyqt@5 from Homebrew.

If you want to build the info module or the graphical user interface, make sure you have the Xcode app installed. Just the Xcode command line tools which are sufficient for Homebrew, will not work with Qt5.

Before running CMake, some environment variables need to be set on the command line. If omitted, the linker will throw a bunch of warnings later:

export SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/\
MacOSX.platform/Developer/SDKs/MacOSX.sdk


If building the info module or with graphical user interface, get the Qt binaries in your Path for CMake to determine its configuration:

export PATH="/usr/local/opt/qt@5/bin:\$PATH"


Homebrew installs all the software under /usr/local. Thus we have to tell cmake where to find Python. Also the Python headers and libraries are not located as they are on Linux and hence they must be specified too. To get rid of a ton of compilation warnings from third party software, we add some dedicated C flags:

cmake . -DPython_INCLUDE_DIRS=/usr/local/opt/python@3.9/Frameworks/\
Python.framework/Versions/Current/include/python3.9/ \
-DPython_LIBRARIES=/usr/local/opt/python@3.9/Frameworks/\
Python.framework/Versions/Current/lib/libpython3.9.dylib \
-DPython_ROOT_DIR=/usr/local/opt/python@3.9/ \
-DBOOST_ROOT=/usr/local \
-DSYS_ROOT=/usr/local \
-DOPTIMIZE=ON \
-DCMAKE_C_FLAGS="-isystem /Applications/Xcode.app/Contents/\
Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/\
Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/\
MacOSX.sdk/System/Library/Frameworks/Security.framework/ \
-DCMAKE_CXX_FLAGS="-isystem /Applications/Xcode.app/\
Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/\
Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/\
MacOSX.sdk/System/Library/Frameworks/Security.framework/ \


Building the Project¶

Type make. If you are using a multi-core machine, you can use the -j flag to run multiple jobs at once.

What’s next?¶

On Linux and macOS, you can start dng from the command-line. The binaries are all located in stage/bin:

stage/bin/dng


or, to start the command-line interpreter:

stage/bin/ost


If you repeatedly use OpenStructure, it is recommended to add /path/to/ost/stage/bin to your path.

To get the newest changes from the central git repository, enter

git pull


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