You are reading the documentation for version 1.9 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 1.10 1.11 2.0 2.1 2.2 2.3 2.3.1 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 (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
  • Compiling an Linking

Installing the Dependencies

OpenStructure uses a bunch of OpenSource libraries. If you haven’t already installed them, please install them now! Where appropriate the minimally required version is given in parentheses.

When you enable support for image processing, you will need:

  • 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:

  • Qt4 (4.5, Qt5 is not supported yet)

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

If you would like to use the molecular mechanics module:

In case you are compiling under Windows you have to install Visualstudio 2008. to compile the dependencies and OpenStructure. We recommend to compile the dependencies manually. Enter the directories where the dependencies are located in Tools->Options->Projects and Solutions->VC++ directories. Choose ‘bin’ directories to enter program paths to cmake, qmake and python, ‘lib’ directories to point to the location(s) of your dependencies.

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 ost.

Note

Some versions of curl have 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 with via -D<opt>=<value>.

On Windows, use Tools -> VisualStudio -> commandline prompt from within VisualStudio.

Flag to choose build generator

CMake supports different build generators. On UNIX, i.e. MacOS X 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, start cmake without parameters.

On Windows you have to explicitly set the build generator to “Visual Studio 9 2008” (or a later version):

cmake -G"Visual Studio 9 2008"

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 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_IMG controls whether to build the image processing module. This will enable support for density maps, and general image processing in 1, 2 an 3 dimensions. By default, this is switched on.
  • 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_LIBRARIES defines the location of the Python library (file name starting with libpython). This must be set if it is not in $PYTHON_ROOT/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_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)
    • Usually, you will receive errors for those variables when executing cmake and set them accordingly as needed.

Build Options

  • OPTIMIZE can be switched on to build an optimized (-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. 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_MESA to use software rendered Mesa instead of hardware GL. By default, this is turned off.
    • 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.

Example Configurations

Generic linux without GUI

The simplest way to compile OpenStructure is to disable the GUI and any dependency to Qt4. You can build an optimized 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.

On some Linux distributions, there are issues with Qt4 and hence it may not be possible to build OpenStructure with GUI support at all. This is for instance known to be an issue with boost versions >= 1.62. We hope to support Qt5 in the next OpenStructure release.

Ubuntu 16.04 with GUI

All the dependencies can be installed from the package manager as follows:

sudo apt-get install cmake sip-dev libtiff-dev libfftw3-dev libeigen3-dev \
             libpng-dev python-all python2.7 python-qt4 libboost-all-dev \
             qt4-qtconfig qt4-qmake libqt4-dev libpng-dev

Now, all dependencies are located in standard locations and cmake will automatically find them without the need to pass any additional parameters. The only exception is the Python library which is put in a different path than expected. Also, we add -DOPTIMIZE, which will tell cmake to build an optimized version of OpenStructure.

cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
        -DOPTIMIZE=ON

Fedora 26 without GUI

All the dependencies can be installed from the package manager as follows:

sudo dnf install cmake eigen3-devel boost-devel libpng-devel python2-devel \
                 fftw-devel libtiff-devel

Here, we compile a version without GUI as follows:

cmake . -DOPTIMIZE=ON -DENABLE_INFO=OFF

macOS with Homebrew without GUI

Homebrew can be used to conveniently install all packages on macOS. Unfortunately, Qt4 is not (officially) supported on macOS Sierra (and newer). Hence, it is not possible to build OpenStructure with GUI support there. Homebrew installs all the software under /usr/local. Thus we have to tell cmake where to find Boost and Python. Also the Python headers and libraries are not located as they are on linux and hence they must be specified too:

cmake . -DPYTHON_INCLUDE_PATH=/usr/local/opt/python/Frameworks/Python.framework/Headers \
        -DPYTHON_LIBRARIES=/usr/local/opt/python/Frameworks/Python.framework/Python \
        -DBOOST_ROOT=/usr/local -DPYTHON_ROOT=/usr/local \
        -DSYS_ROOT=/usr/local -DENABLE_INFO=OFF -DOPTIMIZE=ON

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.

On Windows run ‘Build OpenStructure’ from the build menu.

What’s next?

On Linux and MacOS X, 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.

Getting the newest changes

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

git pull

in your terminal. This will fetch the newest changes.

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