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=== Step-by-step Installation Instructions for OpenBabel on Linux ===
+
== Introduction and requirements ==
  
These instructions describe the installation procedure for OpenBabel 2.0.2. For more recent releases, the version number will be different and you should take this in account when reading the instructions below. In addition, these instructions assume that you have root access. An [[alternative procedure]] may be used if this is not true.
+
Here we describe the compilation and installation procedure for OpenBabel 2.3.0 or newer. For information on installing Open Babel 2.2 series, see [[Install Open Babel 2.2]].  
  
(1) You should download OpenBabel 2.0.2 for Linux by clicking on
+
The following are '''required''' to compile Open Babel:
"Download" under the picture of the fish on the left hand side of this page and choose
+
:: The latest version of the [http://sourceforge.net/project/showfiles.php?group_id=40728&package_id=32894 Open Babel source code]
openbabel-2.0.2.tar.gz. You should save this into a folder called
+
:: A '''C++ compiler''' (like GNU g++ or Intel Compiler icc)
'openbabel' somewhere on your computer.
+
:: A makefile system (like GNU make)
 +
:: '''CMake 2.4''' or newer (available as the ''cmake'' package in Ubuntu, or from the [http://cmake.org/cmake/resources/software.html CMake website])
  
(2) Open a command window, change directory into 'openbabel', and
+
The following are '''optional''' when compiling Open Babel, but if not installed, fewer features will be available:
decompress the downloaded file with following command:
+
:: '''libxml2''' development headers are required to read/write CML files (the ''libxml2-dev'' package in Ubuntu)
 +
:: '''zlib.h''' is required to support reading gzipped files (the ''zlib1g-dev'' package in Ubuntu)
 +
:: If using GCC 3.x to compile (and not GCC 4.x), then the Boost headers are required for certain formats (CML, Chemkin, Chemdraw CDX, MDL RXN and RSMI)
 +
:: '''Eigen''' version 2 is required for some API classes (OBAlign, OBConformerSearch) and plugins (the QEq and QTPIE charge models, the conformer operation). These will not be available otherwise.
 +
::: Eigen may be available through your package manager (the ''libeigen2-dev'' package in Ubuntu). Alternatively, Eigen is available from http://eigen.tuxfamily.org. It doesn’t need to be compiled or installed. Just unzip it and specify its location when configuring cmake (see below) using ''-DEIGEN2_INCLUDE_DIR=whereever''.
 +
 
 +
If you want to build the '''GUI''' (Graphical User Interface), you need the following:
 +
:: '''wxWidgets''' 2.8 (or newer)
 +
:::: Binary packages may be available through your package manager (''wx-common'' and ''wx2.8-headers'' on Ubuntu) or from http://www.wxwidgets.org/downloads/. Otherwise, you could try compiling it yourself from the source code.
 +
 
 +
If you want to use Open Babel using one of the supported '''language bindings''', then the following notes may apply:
 +
:: You need the the Python development libraries to compile the Python bindings (package ''python-dev'' in Ubuntu)
 +
:: You need the the Perl development libraries to compile the Perl bindings (package ''libperl-dev'' in Ubuntu)
 +
:: ''Developer note'': If you are compiling directly from the Subversion repository, then you need to create the Python/Perl bindings yourself. To do so you need to install the latest version of SWIG (at the time of writing, 2.0.1, but there may be a new version).
 +
 
 +
If you want to install globally on your system, you will need root access, and should follow [[Install (source code)#Installing globally with root access | these instructions]]. If you don't have root access or if you simply wish to install in your 'home' area, see [[Install (source code)#Installing locally without root access | Installing locally without root access]].
 +
 
 +
== Installing globally with root access ==
 +
 
 +
(A1) Open a command window, and decompress the downloaded file with the following command:
  
 
<pre>
 
<pre>
tar zxvf openbabel-2.0.2.tar.gz
+
tar zxvf openbabel-2.3.0.tar.gz
 
</pre>
 
</pre>
  
This will create a folder called 'openbabel-2.0.2'.
+
This will create a folder called ''openbabel-2.3.0'' containing the Open Babel source code.
  
(3) You now need to configure and compile openbabel. To do this, change
+
The recommended way of building Open Babel is to use separate source and build folders. Let's call them ''ob-src'' and ''ob-build'':
directory into 'openbabel-2.0.2'. Run the following commands, one after
+
the other
+
  
 
<pre>
 
<pre>
./configure | tee configure.out
+
mv openbabel-2.3.0 ob-src
make | tee make.out
+
mkdir ob-build
 
</pre>
 
</pre>
  
If there are any errors at this point, send an email to the
+
(A2) You now need to configure and compile openbabel. To do this, change
openbabel-discuss mailing list ([email protected].sourceforge.net)
+
directory into ''ob-src''. Run the following commands, one after
and attach the files 'configure.out' and 'make.out'.
+
the other:
 +
<pre>
 +
cd ob-build
 +
cmake ../ob-src 2>&1 | tee cmake.out
 +
make 2>&1 | tee make.out
 +
</pre>
  
(4) If you have root permissions, you should install openbabel globally.
+
If there are any errors at this point, send an email to the [mailto:openbabel[email protected].sourceforge.net openbabel-discuss] mailing list and attach the files ''cmake.out'' and ''make.out''.
As root, run the following command:
+
  
 +
If you look at the output of CMake you can see whether CML and gzip support will be included in Open Babel (see the optional dependencies above).
 +
<pre>#FIXME - INSERT EXAMPLE HERE</pre>
 +
 +
(A3) If you have root permissions, you can install Open Babel globally.
 +
As root, run the following command:
 
<pre>
 
<pre>
 
make install
 
make install
 
</pre>
 
</pre>
  
(5) If you want to use OpenBabel from Python, you now need to compile the python extension. This may require an extra Python package depending on your Linux distribution. For example, for Debian you need the 'python-dev' package (installed using 'apt-get'); for SUSE, you need 'python-devel' (installed using YaST).
+
(A4) If necessary (e.g. ''obabel'' doesn't work), add the location of the installed ''libopenbabel.so'' to the ''LD_LIBRARY_PATH'', in my case:
 +
<pre>
 +
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
 +
</pre>
 +
 
 +
== Installing locally without root access ==
 +
 
 +
If you don't have root access, you can still compile and use Open Babel.
  
Change directory to 'openbabel-2.0.2/scripts/python' and run:
+
(B1) Follow Step A1 above
  
 +
(B2) Make a local directory to install everything into. In this example, I will use the folder ''tree'' in my home directory:
 
<pre>
 
<pre>
python setup.py build
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mkdir /home/noel/tree
 
</pre>
 
</pre>
  
(6) To install the python interface globally, as root type:
+
(B3) Instead of Step A2 above, specify the install directory using the CMake option ''CMAKE_INSTALL_PREFIX'':
 +
<pre>
 +
cmake ../ob-src -DCMAKE_INSTALL_PREFIX=/home/noel/tree 2>&1 | tee cmake.out
 +
make 2>&1 | tee make.out
 +
</pre>
  
 +
(B4) You can now install without root permissions using the following command:
 
<pre>
 
<pre>
python setup.py install
+
make install
 
</pre>
 
</pre>
  
(7) It's all done. Test out the 'openbabel' module by trying some of the
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This installs the ''obabel'' executable (and related tools) to ''/home/noel/tree/bin'' so you need to add this directory to your ''PATH'' in your startup scripts (that is, ''.bashrc'', or whatever):
Python code [[Python#The_openbabel_module  | here]].
+
<pre>
 +
export PATH=$PATH:/home/noel/tree/bin
 +
</pre>
 +
 
 +
(B5) Add the location of the installed ''libopenbabel.so'' to the ''LD_LIBRARY_PATH'', in my case:
 +
<pre>
 +
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/noel/tree/lib
 +
</pre>
 +
 
 +
== Compile bindings for Java, .NET, Perl, Python or Ruby ==
 +
 
 +
To compile and install the bindings for the various languages supported, please see the appropriate page for [[Java]], [[OBDotNet | .NET]], [[Perl]], [[Python]], [[Ruby]].
 +
 
 +
== Compile the development code ==
 +
 
 +
For information on compiling our development code, please see the [[CMake]] page.
 +
 
 +
[[Category:Installation]]

Latest revision as of 05:10, 25 October 2010

Introduction and requirements

Here we describe the compilation and installation procedure for OpenBabel 2.3.0 or newer. For information on installing Open Babel 2.2 series, see Install Open Babel 2.2.

The following are required to compile Open Babel:

The latest version of the Open Babel source code
A C++ compiler (like GNU g++ or Intel Compiler icc)
A makefile system (like GNU make)
CMake 2.4 or newer (available as the cmake package in Ubuntu, or from the CMake website)

The following are optional when compiling Open Babel, but if not installed, fewer features will be available:

libxml2 development headers are required to read/write CML files (the libxml2-dev package in Ubuntu)
zlib.h is required to support reading gzipped files (the zlib1g-dev package in Ubuntu)
If using GCC 3.x to compile (and not GCC 4.x), then the Boost headers are required for certain formats (CML, Chemkin, Chemdraw CDX, MDL RXN and RSMI)
Eigen version 2 is required for some API classes (OBAlign, OBConformerSearch) and plugins (the QEq and QTPIE charge models, the conformer operation). These will not be available otherwise.
Eigen may be available through your package manager (the libeigen2-dev package in Ubuntu). Alternatively, Eigen is available from http://eigen.tuxfamily.org. It doesn’t need to be compiled or installed. Just unzip it and specify its location when configuring cmake (see below) using -DEIGEN2_INCLUDE_DIR=whereever.

If you want to build the GUI (Graphical User Interface), you need the following:

wxWidgets 2.8 (or newer)
Binary packages may be available through your package manager (wx-common and wx2.8-headers on Ubuntu) or from http://www.wxwidgets.org/downloads/. Otherwise, you could try compiling it yourself from the source code.

If you want to use Open Babel using one of the supported language bindings, then the following notes may apply:

You need the the Python development libraries to compile the Python bindings (package python-dev in Ubuntu)
You need the the Perl development libraries to compile the Perl bindings (package libperl-dev in Ubuntu)
Developer note: If you are compiling directly from the Subversion repository, then you need to create the Python/Perl bindings yourself. To do so you need to install the latest version of SWIG (at the time of writing, 2.0.1, but there may be a new version).

If you want to install globally on your system, you will need root access, and should follow these instructions. If you don't have root access or if you simply wish to install in your 'home' area, see Installing locally without root access.

Installing globally with root access

(A1) Open a command window, and decompress the downloaded file with the following command:

tar zxvf openbabel-2.3.0.tar.gz

This will create a folder called openbabel-2.3.0 containing the Open Babel source code.

The recommended way of building Open Babel is to use separate source and build folders. Let's call them ob-src and ob-build:

mv openbabel-2.3.0 ob-src
mkdir ob-build

(A2) You now need to configure and compile openbabel. To do this, change directory into ob-src. Run the following commands, one after the other:

cd ob-build
cmake ../ob-src 2>&1 | tee cmake.out
make 2>&1 | tee make.out

If there are any errors at this point, send an email to the openbabel-discuss mailing list and attach the files cmake.out and make.out.

If you look at the output of CMake you can see whether CML and gzip support will be included in Open Babel (see the optional dependencies above).

#FIXME - INSERT EXAMPLE HERE

(A3) If you have root permissions, you can install Open Babel globally. As root, run the following command:

make install

(A4) If necessary (e.g. obabel doesn't work), add the location of the installed libopenbabel.so to the LD_LIBRARY_PATH, in my case:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

Installing locally without root access

If you don't have root access, you can still compile and use Open Babel.

(B1) Follow Step A1 above

(B2) Make a local directory to install everything into. In this example, I will use the folder tree in my home directory:

mkdir /home/noel/tree

(B3) Instead of Step A2 above, specify the install directory using the CMake option CMAKE_INSTALL_PREFIX:

cmake ../ob-src -DCMAKE_INSTALL_PREFIX=/home/noel/tree 2>&1 | tee cmake.out
make 2>&1 | tee make.out

(B4) You can now install without root permissions using the following command:

make install

This installs the obabel executable (and related tools) to /home/noel/tree/bin so you need to add this directory to your PATH in your startup scripts (that is, .bashrc, or whatever):

export PATH=$PATH:/home/noel/tree/bin

(B5) Add the location of the installed libopenbabel.so to the LD_LIBRARY_PATH, in my case:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/noel/tree/lib

Compile bindings for Java, .NET, Perl, Python or Ruby

To compile and install the bindings for the various languages supported, please see the appropriate page for Java, .NET, Perl, Python, Ruby.

Compile the development code

For information on compiling our development code, please see the CMake page.