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Software prerequisites and installation procedure
Oracle's Java proprietary implementation is required for running this software under Linux : this can be downloaded at : http://www.oracle.com/technetwork/java/javase/downloads/index.html
Download the JRE if you just plan to use the software, or the JDK if you plan some Java software development.
Check this page for instructions if you are using either Fedora 12 to 20 or RedHat/CentOS 5.10 to 6.5 : http://www.if-not-true-then-false.com/2010/install-sun-oracle-java-jdk-jre-7-on-fedora-centos-red-hat-rhel
Please follow all the steps of the procedure, and do not forget the step alternatives --config java for enabling the use of the Oracle implementation.
Check this page for instructions if you are using Ubuntu : http://www.wikihow.com/Install-Oracle-Java-on-Ubuntu-Linux
Open Babel is a toolkit for manipulating chemical data : here it is mainly used for chemical coordinates file conversion. Some Linux distributions provide binary compiled versions.
Otherwise check http://openbabel.org/wiki/Main_Page for instructions and manual download and compiling.
This software allows you to visualize the resulting multipoles within VMD.
If you need to install VMD : http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD and see http://www.ks.uiuc.edu/Research/vmd/current/docs.html for installation instructions.
You need to have a Python 2.7 scripting environment installed : this is already the case for most of the Linux distributions, if not please check the documentation pages of your distribution for more instructions.
Alternatively, you can download and compile Python 2.7 by yourself : http://www.python.org/download/releases/2.7/}{http://www.python.org/download/releases/2.7
NumPy and SciPy are two Python modules used for scientific and mathematics computations. Most of the Linux distributions will provide a way of directly installing binary versions of those libraries.
Otherwise, check http://www.numpy.org and http://www.scipy.org for more instructions or for a manual install.
RDKit is an open source toolkit for cheminformatics. See http://sourceforge.net/projects/rdkit/files for downloading the sources and http://rdkit.org/docs/index.html for installation instructions.
If you need to compile RDKit by yourself, you will require several packages:
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Python development libraries : under Ubuntu, install with apt-get install python-dev under Fedora or CentOS/RHEL install with yum install python-devel, if you compiled Python by yourself you should have it.
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Flex and Bison and Cmake, 3 packages used for building the software suite: yum install flex bison cmake or apt-get install flex bison cmake. If you need to install the software manually, check: http://www.gnu.org/software/bison or http://flex.sourceforge.net or http://www.cmake.org/cmake/resources/software.html or
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The boost library, a collection of tools commonly used in modern programming: install with yum install boost boost-devel or apt-get install libboost-all-dev. Alternatively for a manual install, see http://www.boost.org/users/download
Before running the make command and after using cmake (see RDKit docs), run cmake -D RDK_INSTALL_INTREE=OFF . for choosing as installation path the default /usr/local
Once the software is installed you need to define the two following environment variables : export PYTHONPATH=/usr/local/lib64/python2.7/site-packages/ and export LD_LIBRARY_PATH=/usr/local/lib/
Then open a python2.7 interpreter and try the following two commands to validate the installation: import rdkit and from rdkit import Chem
If no error message is displayed RDKit can be properly used by the FittingWizard