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<h3><a href="index.html">Table Of Contents</a></h3>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Overview.html">An overview of the RDKit</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#linux-and-the-mac">Linux and the Mac</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#installation-from-repositories">Installation from repositories</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#ubuntu-12-04-and-later">Ubuntu 12.04 and later</a></li>
<li class="toctree-l4"><a class="reference internal" href="#fedora-centos-and-rhel">Fedora, CentOS, and RHEL</a></li>
<li class="toctree-l4"><a class="reference internal" href="#macos">MacOS</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="#building-from-source">Building from Source</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#prerequisites">Prerequisites</a></li>
<li class="toctree-l4"><a class="reference internal" href="#building-the-rdkit">Building the RDKit</a></li>
<li class="toctree-l4"><a class="reference internal" href="#testing-the-build-optional-but-recommended">Testing the build (optional, but recommended)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#advanced">Advanced</a></li>
<li class="toctree-l4"><a class="reference internal" href="#frequently-encountered-problems">Frequently Encountered Problems</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#windows">Windows</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id1">Prerequisites</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#recommended-extras">Recommended extras</a></li>
</ul>
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<li class="toctree-l3"><a class="reference internal" href="#installation-of-rdkit-binaries">Installation of RDKit binaries</a></li>
<li class="toctree-l3"><a class="reference internal" href="#installation-from-source">Installation from source</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#extra-software-to-install">Extra software to install</a></li>
<li class="toctree-l4"><a class="reference internal" href="#setup-and-preparation">Setup and Preparation</a></li>
<li class="toctree-l4"><a class="reference internal" href="#building-from-the-command-line-recommended">Building from the command line (recommended)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#building-the-code-using-guis-not-recommended">Building the Code Using GUIs (not recommended)</a></li>
<li class="toctree-l4"><a class="reference internal" href="#id2">Testing the Build (optional, but recommended)</a></li>
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<li class="toctree-l1"><a class="reference internal" href="GettingStartedInPython.html">Getting Started with the RDKit in Python</a></li>
<li class="toctree-l1"><a class="reference internal" href="RDKit_Book.html">The RDKit Book</a></li>
<li class="toctree-l1"><a class="reference internal" href="Cookbook.html">RDKit Cookbook</a></li>
<li class="toctree-l1"><a class="reference internal" href="Cartridge.html">The RDKit database cartridge</a></li>
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<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<p>Below a number of installation recipies is presented, with varying degree of
complexity.</p>
<div class="section" id="linux-and-the-mac">
<h2>Linux and the Mac<a class="headerlink" href="#linux-and-the-mac" title="Permalink to this headline">¶</a></h2>
<div class="section" id="installation-from-repositories">
<h3>Installation from repositories<a class="headerlink" href="#installation-from-repositories" title="Permalink to this headline">¶</a></h3>
<div class="section" id="ubuntu-12-04-and-later">
<h4>Ubuntu 12.04 and later<a class="headerlink" href="#ubuntu-12-04-and-later" title="Permalink to this headline">¶</a></h4>
<p>Thanks to the efforts of the Debichem team, RDKit is available via the Ubuntu repositories.
To install:</p>
<div class="highlight-python"><div class="highlight"><pre>sudo apt-get install python-rdkit librdkit1 rdkit-data
</pre></div>
</div>
</div>
<div class="section" id="fedora-centos-and-rhel">
<h4>Fedora, CentOS, and RHEL<a class="headerlink" href="#fedora-centos-and-rhel" title="Permalink to this headline">¶</a></h4>
<p>Gianluca Sforna creates binary RPMs that can be found here: <<a class="reference external" href="http://giallu.fedorapeople.org/rdkit-20XX.XX/">http://giallu.fedorapeople.org/rdkit-20XX.XX/</a>>_</p>
</div>
<div class="section" id="macos">
<h4>MacOS<a class="headerlink" href="#macos" title="Permalink to this headline">¶</a></h4>
<p>Eddie Cao has produced a homebrew formula that can be used to easily build the RDKit <<a class="reference external" href="https://github.com/rdkit/homebrew-rdkit">https://github.com/rdkit/homebrew-rdkit</a>>_</p>
</div>
</div>
<div class="section" id="building-from-source">
<h3>Building from Source<a class="headerlink" href="#building-from-source" title="Permalink to this headline">¶</a></h3>
<div class="section" id="prerequisites">
<h4>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline">¶</a></h4>
<div class="section" id="installing-prerequisites-as-packages">
<h5>Installing prerequisites as packages<a class="headerlink" href="#installing-prerequisites-as-packages" title="Permalink to this headline">¶</a></h5>
<div class="section" id="ubuntu-and-other-debian-derived-systems">
<h6>Ubuntu and other debian-derived systems<a class="headerlink" href="#ubuntu-and-other-debian-derived-systems" title="Permalink to this headline">¶</a></h6>
<p>Install the following packages using apt-get:</p>
<div class="highlight-python"><div class="highlight"><pre>flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev
libboost-dev libboost-python-dev libboost-regex-dev
</pre></div>
</div>
</div>
<div class="section" id="fedora-centos-5-7-and-rhel">
<h6>Fedora, CentOS (5.7+), and RHEL<a class="headerlink" href="#fedora-centos-5-7-and-rhel" title="Permalink to this headline">¶</a></h6>
<p>Install the following packages using yum:</p>
<div class="highlight-python"><div class="highlight"><pre>cmake tk-devel readline-devel zlib-devel bzip2-devel sqlite-devel @development-tools
</pre></div>
</div>
<p>Packages to install from source (not required on RHEL/CentOS 6.x):</p>
<blockquote>
<div><ul class="simple">
<li>python 2.7 : use ./configure CFLAGS=-fPIC –enable-unicode=ucs4 –enable-shared</li>
<li>numpy : do export LD_LIBRARY_PATH=”/usr/local/lib” before python setup.py install</li>
<li>boost 1.48.0 or later: do ./bootstrap.sh –with-libraries=python,regex; ./b2; ./b2 install</li>
</ul>
</div></blockquote>
</div>
<div class="section" id="older-versions-of-centos">
<h6>Older versions of CentOS<a class="headerlink" href="#older-versions-of-centos" title="Permalink to this headline">¶</a></h6>
<p>Here things are more difficult. Check this wiki page for
information: <a class="reference external" href="https://code.google.com/p/rdkit/wiki/BuildingOnCentOS">https://code.google.com/p/rdkit/wiki/BuildingOnCentOS</a></p>
</div>
</div>
<div class="section" id="installing-prerequisites-from-source">
<h5>Installing prerequisites from source<a class="headerlink" href="#installing-prerequisites-from-source" title="Permalink to this headline">¶</a></h5>
<blockquote>
<div><ul>
<li><p class="first">Required packages:</p>
<ul>
<li><p class="first">cmake. You need version 2.6 (or more recent). <a class="reference external" href="http://www.cmake.org">http://www.cmake.org</a> if your linux distribution doesn’t have an appropriate package.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">It seems that v2.8 is a better bet than v2.6. It might be worth compiling your own copy of v2.8 even if v2.6 is already installed.</p>
</div>
</li>
<li><p class="first">The following are required if you are planning on using the Python wrappers</p>
<blockquote>
<div><ul>
<li><p class="first">The python headers. This probably means that you need to install the python-dev package (or whatever it’s called) for your linux distribution.</p>
</li>
<li><p class="first">sqlite3. You also need the shared libraries. This may require that you install a sqlite3-dev package.</p>
</li>
<li><p class="first">You need to have numpy (<a class="reference external" href="http://www.scipy.org/NumPy">http://www.scipy.org/NumPy</a>) installed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">for building with XCode4 on the MacOS – there seems to be a problem with the version of numpy that comes with XCode4. Please see below in the (see <a class="reference internal" href="#faq"><em>Frequently Encountered Problems</em></a>) section for a workaround.</p>
</div>
</li>
</ul>
</div></blockquote>
</li>
</ul>
</li>
<li><p class="first">Optional packages</p>
<ul class="simple">
<li>If you would like to install the RDKit InChI support (first available in the Q2 2011 release), follow the instructions in $RDBASE/External/INCHI-API to get a copy of the InChI source and put it in the appropriate place.</li>
</ul>
</li>
</ul>
</div></blockquote>
<div class="section" id="installing-boost">
<h6>Installing Boost<a class="headerlink" href="#installing-boost" title="Permalink to this headline">¶</a></h6>
<p>If your linux distribution has a boost-devel package including the python and regex libraries, you can use that and save yourself the steps below.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>if you <em>do</em> have a version of the boost libraries pre-installed and you want to use your own version, be careful when you build the code. We’ve seen at least one example on a Fedora system where cmake compiled using a user-installed version of boost and then linked against the system version. This led to segmentation faults. There is a workaround for this below in the (see <a class="reference internal" href="#faq"><em>Frequently Encountered Problems</em></a>) section.</p>
<ul class="last">
<li><p class="first">download the boost source distribution from <a class="reference external" href="http://www.boost.org">the boost web site</a></p>
</li>
<li><p class="first">extract the source somewhere on your machine (e.g. <tt class="docutils literal"><span class="pre">/usr/local/src/boost_1_45_0</span></tt>)</p>
</li>
<li><p class="first">build the required boost libraries:</p>
<ul class="simple">
<li><tt class="docutils literal"><span class="pre">cd</span> <span class="pre">$BOOST</span></tt></li>
<li>If you want to use the python wrappers: <tt class="docutils literal"><span class="pre">./bootstrap.sh</span> <span class="pre">--with-libraries=python,regex</span></tt></li>
<li>If not using the python wrappers: <tt class="docutils literal"><span class="pre">./bootstrap.sh</span> <span class="pre">--with-libraries=regex</span></tt></li>
<li>Building on 32 bit systems: <tt class="docutils literal"><span class="pre">./b2</span> <span class="pre">install</span></tt></li>
<li>Building on 64 bit systems: <tt class="docutils literal"><span class="pre">./b2</span> <span class="pre">address-model=64</span> <span class="pre">cflags=-fPIC</span> <span class="pre">cxxflags=-fPIC</span> <span class="pre">install</span></tt></li>
</ul>
<p>If you have any problems with this step, check the boost <a class="reference external" href="http://www.boost.org/more/getting_started/unix-variants.html">installation instructions</a>.</p>
</li>
</ul>
</div>
</div>
</div>
</div>
<div class="section" id="building-the-rdkit">
<h4>Building the RDKit<a class="headerlink" href="#building-the-rdkit" title="Permalink to this headline">¶</a></h4>
<p>Fetch the source, here as tar.gz but you could use git as well:</p>
<div class="highlight-python"><div class="highlight"><pre> wget http://downloads.sourceforge.net/project/rdkit/rdkit/QX_20XX/RDKit_20XX_XX_X.tgz
* Ensure that the prerequisites are installed
* environment variables:
* RDBASE: the root directory of the RDKit distribution (e.g. ~/RDKit)
* *Linux:* LD_LIBRARY_PATH: make sure it includes $RDBASE/lib and wherever the boost shared libraries were installed
* *Mac:* DYLD_LIBRARY_PATH: make sure it includes $RDBASE/lib and wherever the boost shared libraries were installed
* The following are required if you are planning on using the Python wrappers:
* PYTHONPATH: make sure it includes $RDBASE
* Building:
* cd to $RDBASE
* ``mkdir build``
* ``cd build``
* ``cmake ..`` : See the section below on configuring the build if you need to specify a non-default version of python or if you have boost in a non-standard location
* ``make`` : this builds all libraries, regression tests, and wrappers (by default).
* ``make install``
</pre></div>
</div>
<p>See below for a list of <a class="reference internal" href="#faq"><em>Frequently Encountered Problems</em></a> and solutions.</p>
</div>
<div class="section" id="testing-the-build-optional-but-recommended">
<h4>Testing the build (optional, but recommended)<a class="headerlink" href="#testing-the-build-optional-but-recommended" title="Permalink to this headline">¶</a></h4>
<blockquote>
<div><ul class="simple">
<li>cd to $RDBASE/build and do <tt class="docutils literal"><span class="pre">ctest</span></tt></li>
<li>you’re done!</li>
</ul>
</div></blockquote>
</div>
<div class="section" id="advanced">
<h4>Advanced<a class="headerlink" href="#advanced" title="Permalink to this headline">¶</a></h4>
<div class="section" id="specifying-an-alternate-boost-installation">
<h5>Specifying an alternate Boost installation<a class="headerlink" href="#specifying-an-alternate-boost-installation" title="Permalink to this headline">¶</a></h5>
<p>You need to tell cmake where to find the boost libraries and header files:</p>
<p>If you have put boost in /opt/local, the cmake invocation would look like:</p>
<div class="highlight-python"><div class="highlight"><pre>cmake -DBOOST_ROOT=/opt/local ..
</pre></div>
</div>
</div>
<div class="section" id="specifying-an-alternate-python-installation">
<h5>Specifying an alternate Python installation<a class="headerlink" href="#specifying-an-alternate-python-installation" title="Permalink to this headline">¶</a></h5>
<p>You need to tell cmake where to find the python library it should link against and the python header files.</p>
<p>Here’s a sample command line:</p>
<div class="highlight-python"><div class="highlight"><pre>cmake -D PYTHON_LIBRARY=/usr/lib/python2.5/config/libpython2.5.a -D PYTHON_INCLUDE_DIR=/usr/include/python2.5/ -D PYTHON_EXECUTABLE=/usr/bin/python ..
</pre></div>
</div>
<p>The <tt class="docutils literal"><span class="pre">PYTHON_EXECUTABLE</span></tt> part is optional if the correct python is the first version in your PATH.</p>
</div>
<div class="section" id="disabling-the-python-wrappers">
<h5>Disabling the Python wrappers<a class="headerlink" href="#disabling-the-python-wrappers" title="Permalink to this headline">¶</a></h5>
<p>You can completely disable building of the python wrappers by setting the configuration variable RDK_BUILD_PYTHON_WRAPPERS to nil:</p>
<div class="highlight-python"><div class="highlight"><pre>cmake -D RDK_BUILD_PYTHON_WRAPPERS= ..
</pre></div>
</div>
</div>
<div class="section" id="building-the-java-wrappers">
<h5>Building the Java wrappers<a class="headerlink" href="#building-the-java-wrappers" title="Permalink to this headline">¶</a></h5>
<p><em>Additional Requirements</em></p>
<ul class="simple">
<li>SWIG v2.0.x: <a class="reference external" href="http://www.swig.org">http://www.swig.org</a></li>
<li>Junit: get a copy of the junit .jar file from <a class="reference external" href="https://github.com/KentBeck/junit/downloads">https://github.com/KentBeck/junit/downloads</a> and put it in the directory <tt class="docutils literal"><span class="pre">$RDBASE/External/java_lib</span></tt> (you will need to create the directory) and rename it to junit.jar.</li>
</ul>
<p><em>Building</em></p>
<blockquote>
<div><ul class="simple">
<li>When you invoke cmake add <tt class="docutils literal"><span class="pre">-D</span> <span class="pre">RDK_BUILD_SWIG_WRAPPERS=ON</span></tt> to the arguments. For example: <tt class="docutils literal"><span class="pre">cmake</span> <span class="pre">-D</span> <span class="pre">RDK_BUILD_SWIG_WRAPPERS=ON</span> <span class="pre">..</span></tt></li>
<li>Build and install normally using <cite>make</cite>. The directory <tt class="docutils literal"><span class="pre">$RDBASE/Code/JavaWrappers/gmwrapper</span></tt> will contain the three required files: libGraphMolWrap.so (libGraphMolWrap.jnilib on the Mac), org.RDKit.jar, and org.RDKitDoc.jar.</li>
</ul>
</div></blockquote>
<p><em>Using the wrappers</em></p>
<p>To use the wrappers, the three files need to be in the same directory, and that should be on your CLASSPATH and in the java.library.path. An example using jython:</p>
<div class="highlight-python"><div class="highlight"><pre>% CLASSPATH=$CLASSPATH:$RDBASE/Code/JavaWrappers/gmwrapper/org.RDKit.jar; jython -Djava.library.path=$RDBASE/Code/JavaWrappers/gmwrapper
Jython 2.2.1 on java1.6.0_20
Type "copyright", "credits" or "license" for more information.
>>> from org.RDKit import *
>>> from java import lang
>>> lang.System.loadLibrary('GraphMolWrap')
>>> m = RWMol.MolFromSmiles('c1ccccc1')
>>> m.getNumAtoms()
6L
</pre></div>
</div>
</div>
</div>
<div class="section" id="frequently-encountered-problems">
<span id="faq"></span><h4>Frequently Encountered Problems<a class="headerlink" href="#frequently-encountered-problems" title="Permalink to this headline">¶</a></h4>
<p>In each case I’ve replaced specific pieces of the path with <tt class="docutils literal"><span class="pre">...</span></tt>.</p>
<p><em>Problem:</em></p>
<div class="highlight-python"><div class="highlight"><pre>Linking CXX shared library libSLNParse.so
/usr/bin/ld: .../libboost_regex.a(cpp_regex_traits.o): relocation R_X86_64_32S against `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage' can not be used when making a shared object; recompile with -fPIC
.../libboost_regex.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
make: *** [all] Error 2
</pre></div>
</div>
<p><em>Solution:</em></p>
<p>Add this to the arguments when you call cmake: <tt class="docutils literal"><span class="pre">-DBoost_USE_STATIC_LIBS=OFF</span></tt></p>
<p>More information here: <a class="reference external" href="http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html">http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html</a></p>
<hr class="docutils" />
<p><em>Problem:</em></p>
<div class="highlight-python"><div class="highlight"><pre> .../Code/GraphMol/Wrap/EditableMol.cpp:114: instantiated from here
.../boost/type_traits/detail/cv_traits_impl.hpp:37: internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
Preprocessed source stored into /tmp/ccgSaXge.out file, please attach this to your bugreport.
make[2]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o] Error 1
make[1]: *** [Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/all] Error 2
make: *** [all] Error 2
</pre></div>
</div>
<p><em>Solution:</em></p>
<p>Add <tt class="docutils literal"><span class="pre">#define</span> <span class="pre">BOOST_PYTHON_NO_PY_SIGNATURES</span></tt> at the top of <tt class="docutils literal"><span class="pre">Code/GraphMol/Wrap/EditableMol.cpp</span></tt></p>
<p>More information here: <a class="reference external" href="http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01178.html">http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01178.html</a></p>
<hr class="docutils" />
<p><em>Problem:</em></p>
<p>Your system has a version of boost installed in /usr/lib, but you would like to force the RDKit to use a more recent one.</p>
<p><em>Solution:</em></p>
<p>This can be solved by using cmake version 2.8.3 (or more recent) and providing the <tt class="docutils literal"><span class="pre">-D</span> <span class="pre">Boost_NO_SYSTEM_PATHS=ON</span></tt> argument:</p>
<div class="highlight-python"><div class="highlight"><pre>cmake -D BOOST_ROOT=/usr/local -D Boost_NO_SYSTEM_PATHS=ON ..
</pre></div>
</div>
<hr class="docutils" />
<p><em>Problem:</em></p>
<p>Building on the Mac with XCode 4</p>
<p>The problem seems to be caused by the version of numpy that is distributed with XCode 4, so you need to build a fresh copy.</p>
<p><em>Solution:</em>
Get a copy of numpy and build it like this as root:
as root:</p>
<div class="highlight-python"><div class="highlight"><pre>export MACOSX_DEPLOYMENT_TARGET=10.6
export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch x86_64"
export CFLAGS="-arch x86_64"
ln -s /usr/bin/gcc /usr/bin/gcc-4.2
ln -s /usr/bin/g++ /usr/bin/g++-4.2
python setup.py build
python setup.py install
</pre></div>
</div>
<p>Be sure that the new numpy is used in the build:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">PYTHON_NUMPY_INCLUDE_PATH</span> <span class="o">/</span><span class="n">Library</span><span class="o">/</span><span class="n">Python</span><span class="o">/</span><span class="mf">2.6</span><span class="o">/</span><span class="n">site</span><span class="o">-</span><span class="n">packages</span><span class="o">/</span><span class="n">numpy</span><span class="o">/</span><span class="n">core</span><span class="o">/</span><span class="n">include</span>
</pre></div>
</div>
<p>and is at the beginning of the PYTHONPATH:</p>
<div class="highlight-python"><div class="highlight"><pre>export PYTHONPATH="/Library/Python/2.6/site-packages:$PYTHONPATH"
</pre></div>
</div>
<p>Now it’s safe to build boost and the RDKit.</p>
</div>
</div>
</div>
<div class="section" id="windows">
<h2>Windows<a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h2>
<div class="section" id="id1">
<h3>Prerequisites<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li>Python 2.7 (from <a class="reference external" href="http://www.python.org/">http://www.python.org/</a>)</li>
<li>numpy (from <a class="reference external" href="http://numpy.scipy.org/">http://numpy.scipy.org/</a> or use <tt class="docutils literal"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">numpy</span></tt>). Binaries for win64 are available here: <a class="reference external" href="http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy">http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy</a></li>
<li>PIL: (from <a class="reference external" href="http://www.pythonware.com/products/pil/index.htm">http://www.pythonware.com/products/pil/index.htm</a> or use <tt class="docutils literal"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">PIL</span></tt>)</li>
</ul>
</div></blockquote>
<div class="section" id="recommended-extras">
<h4>Recommended extras<a class="headerlink" href="#recommended-extras" title="Permalink to this headline">¶</a></h4>
<blockquote>
<div><ul class="simple">
<li>aggdraw: a library for high-quality drawing in Python. Instructions for downloading are here: <a class="reference external" href="http://effbot.org/zone/aggdraw-index.htm">http://effbot.org/zone/aggdraw-index.htm</a> The new (as of May 2008) drawing code has been tested with v1.2a3 of aggdraw. Despite the alpha label, the code is stable and functional.</li>
<li>matplotlib: a library for scientific plotting from Python. <a class="reference external" href="http://matplotlib.sourceforge.net/">http://matplotlib.sourceforge.net/</a></li>
<li>ipython : a very useful interactive shell (and much more) for Python. <a class="reference external" href="http://ipython.scipy.org/dist/">http://ipython.scipy.org/dist/</a></li>
<li>win32all: Windows extensions for Python. <a class="reference external" href="http://sourceforge.net/projects/pywin32/">http://sourceforge.net/projects/pywin32/</a></li>
</ul>
</div></blockquote>
</div>
</div>
<div class="section" id="installation-of-rdkit-binaries">
<h3>Installation of RDKit binaries<a class="headerlink" href="#installation-of-rdkit-binaries" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li>Get the appropriate windows binary build from: <<a class="reference external" href="https://sourceforge.net/projects/rdkit/files/rdkit/">https://sourceforge.net/projects/rdkit/files/rdkit/</a>>_</li>
<li>Extract the zip file somewhere without a space in the name, i.e. <tt class="docutils literal"><span class="pre">c:/</span></tt></li>
<li>The rest of this will assume that the installation is in <tt class="docutils literal"><span class="pre">c:/RDKit_2012_12_1</span></tt></li>
<li>Set the following environment variables:
* RDBASE: <tt class="docutils literal"><span class="pre">c:/RDKit_2012_12_1</span></tt>
* PYTHONPATH: <tt class="docutils literal"><span class="pre">%RDBASE%</span></tt> if there is already a PYTHONPATH, put <tt class="docutils literal"><span class="pre">;%RDBASE%</span></tt> at the end.
* PATH: add <tt class="docutils literal"><span class="pre">;%RDBASE%/lib</span></tt> to the end</li>
</ul>
</div></blockquote>
<p>In Win7 systems, you may run into trouble due to missing DLLs, see one thread from the mailing list:
<a class="reference external" href="http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01632.html">http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01632.html</a>
You can download the missing DLLs from here: <a class="reference external" href="http://www.microsoft.com/en-us/download/details.aspx?id=5555">http://www.microsoft.com/en-us/download/details.aspx?id=5555</a></p>
</div>
<div class="section" id="installation-from-source">
<h3>Installation from source<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">¶</a></h3>
<div class="section" id="extra-software-to-install">
<h4>Extra software to install<a class="headerlink" href="#extra-software-to-install" title="Permalink to this headline">¶</a></h4>
<blockquote>
<div><ul class="simple">
<li>Microsoft Visual C++ : The Express version has everything
necessary and can be downloaded for free
(<a class="reference external" href="http://www.microsoft.com/express/download/">http://www.microsoft.com/express/download/</a>). This
is a big installation and will take a while. The RDKit has been
successfully built with all version of visual c++ since 6.0, so
the current version of VC++ (2010 as of this writing) should be
fine.</li>
<li>cmake : (<a class="reference external" href="http://www.cmake.org/cmake/resources/software.html">http://www.cmake.org/cmake/resources/software.html</a>) should be installed.</li>
<li>boost : It is strongly recommended to download and use a
precompiled version of the boost libraries from
<a class="reference external" href="http://sourceforge.net/projects/boost/files/boost-binaries/">http://sourceforge.net/projects/boost/files/boost-binaries/</a> . When you run the installer,
the only binary libraries you need are python, regex, and system.
If you want to install boost from source, download a copy from
<a class="reference external" href="http://www.boost.org">http://www.boost.org</a> and follow the instructions
in the “Getting Started” section of the documentation. Make sure
the libraries and headers are installed to c:boost</li>
<li>a git client : <em>This is only necessary if you are planning
on building development versions of the RDKit.</em> This can be downloaded from
<a class="reference external" href="http://git-scm.com/downloads">http://git-scm.com/downloads</a> .</li>
<li>Optional packages<ul>
<li>If you would like to install the RDKit InChI support, follow the
instructions in $RDBASE/External/INCHI-API/README to get a copy
of the InChI source and put it in the appropriate place.</li>
<li>If you would like to install the RDKit Avalon toolkit support,
follow the instructions in $RDBASE/External/AvalonTool/README to
get a copy of the Avalon toolkit source and put it in the
appropriate place.</li>
</ul>
</li>
</ul>
</div></blockquote>
</div>
<div class="section" id="setup-and-preparation">
<h4>Setup and Preparation<a class="headerlink" href="#setup-and-preparation" title="Permalink to this headline">¶</a></h4>
<p>This section assumes that python is installed in <tt class="docutils literal"><span class="pre">c:\Python27</span></tt>, that the
boost libraries have been installed to <tt class="docutils literal"><span class="pre">c:\boost</span></tt>, and that
you will build the RDKit from a directory named <tt class="docutils literal"><span class="pre">c:\RDKit</span></tt>. If any of
these conditions is not true, just change the corresponding paths.</p>
<blockquote>
<div><ul class="simple">
<li>If you install things in paths that have spaces in their names,
be sure to use quotes properly in your environment variable
definitions.</li>
<li>If you are planning on using a development version of the RDKit:
get a copy of the current RDKit source using git. If you’re
using the command-line client the command is: <tt class="docutils literal"><span class="pre">git</span> <span class="pre">clone</span>
<span class="pre">https://github.com/rdkit/rdkit.git</span> <span class="pre">c:\RDKit</span></tt></li>
<li>If you are planning on using a released version of the RDKit : get
a copy of the most recent release and extract it into the directory <tt class="docutils literal"><span class="pre">c:\RDKit</span></tt></li>
<li>Set the required environment variables (you can set this in cygwin
or in windows. If you set them in windows, be sure to restart your
cygwin window)<ul>
<li><tt class="docutils literal"><span class="pre">RDBASE</span> <span class="pre">=</span> <span class="pre">c:\RDKit</span></tt></li>
<li>Make sure <tt class="docutils literal"><span class="pre">c:\Python27</span></tt> is in your PATH</li>
<li>Make sure <tt class="docutils literal"><span class="pre">c:\RDKit\lib</span></tt> is in your PATH</li>
<li>Make sure <tt class="docutils literal"><span class="pre">c:\boost\lib</span></tt> is in your PATH.</li>
<li>Make sure <tt class="docutils literal"><span class="pre">c:\RDKit</span> <span class="pre">is</span></tt> in your PYTHONPATH</li>
</ul>
</li>
</ul>
</div></blockquote>
</div>
<div class="section" id="building-from-the-command-line-recommended">
<h4>Building from the command line (recommended)<a class="headerlink" href="#building-from-the-command-line-recommended" title="Permalink to this headline">¶</a></h4>
<blockquote>
<div><ul class="simple">
<li>Create a directory <tt class="docutils literal"><span class="pre">c:\RDKit\build</span></tt> and cd into it</li>
<li>Run cmake. Here’s an example basic command line for 64bit windows that assumes the InChI and
Avalon toolkit sources are available (see above):
<tt class="docutils literal"><span class="pre">cmake</span> <span class="pre">-DRDK_BUILD_PYTHON_WRAPPERS=0N</span> <span class="pre">-DAVALONTOOLS_DIR=c:/avalontoolkit_beta/sourcedistribution</span> <span class="pre">-DBOOST_ROOT=c:/boost</span> <span class="pre">-DRDK_BUILD_INCHI_SUPPORT=ON</span> <span class="pre">-DRDK_BUILD_AVALON_SUPPORT=ON</span> <span class="pre">-G"Visual</span> <span class="pre">Studio</span> <span class="pre">10</span> <span class="pre">Win64"</span> <span class="pre">..</span></tt></li>
<li>Build the code. Here’s an example command line:
<tt class="docutils literal"><span class="pre">c:/Windows/Microsoft.NET/Framework64/v4.0.30319/MSBuild.exe</span> <span class="pre">/m:4</span> <span class="pre">/p:Configuration=Release</span> <span class="pre">INSTALL.vcxproj</span></tt></li>
</ul>
</div></blockquote>
</div>
<div class="section" id="building-the-code-using-guis-not-recommended">
<h4>Building the Code Using GUIs (not recommended)<a class="headerlink" href="#building-the-code-using-guis-not-recommended" title="Permalink to this headline">¶</a></h4>
<blockquote>
<div><ul class="simple">
<li>Environment variables: if cmake complains about not being able to find it, define the environment variable BOOST_ROOT to point to the directory containing the boost source.</li>
<li>Configure the build:<ul>
<li>Start the cmake gui</li>
<li>tell it where the source code is (e.g. c:/RDKit) and where to build the binaries (recommended: c:/RDKit/build)</li>
<li>click “Configure”, select your compiler, and wait until the
basic configuration is complete, you’ll see a bunch of red entries in the main windows.</li>
<li>click “Configure” again</li>
<li>click “Generate”</li>
</ul>
</li>
<li>Build:<ul>
<li>open the solution file that cmake created (c:/RDKit/build/RDKit.sln) with Visual Studio.</li>
<li>check to be sure that you’re building a Release build (for some reason CMake produces solution files that default to doing a Debug build)</li>
<li>build the “ALL_BUILD” target; this will take a while and generate warnings, but there should be no errors. Note: if you are building the SWIG wrappers you may get an error the first time you try to build them. If you see this error, try building ALL_BUILD again; it should work the second time.</li>
<li>build the “INSTALL” target</li>
</ul>
</li>
</ul>
</div></blockquote>
</div>
<div class="section" id="id2">
<h4>Testing the Build (optional, but recommended)<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h4>
<blockquote>
<div><ul class="simple">
<li>cd to <tt class="docutils literal"><span class="pre">c:\RDKit\build</span></tt> and run ctest.</li>
<li>you’re done!</li>
</ul>
</div></blockquote>
</div>
</div>
</div>
</div>
</div>
</div>
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