I make extensive use of this brilliant piece of cheminformatics software (RD)kit, and it has saved me writing my own Molecule, Atom, Bond, Conformer, Fingerprint, SimilarityMetric, Descriptor etc. classes time and time again. It is really neat, and works with C++ and python (and Java I think). Here are the instructions on how to install it on a relatively recent Ubuntu version (12.04 / 12.10 / 13.04 / 13.10 / 14.04 / 14.10).
Pre-requisite software (this is why I love Debian based systems)
sudo apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost-dev libboost-python-dev libboost-regex-dev
Get the latest RDKit goodie from here (watch out – version number has been replaced by ‘X’ below)
Unzip the beast, save it to
sudo tar xzvf RDKit_20XX_XX_X.tgz -C /opt
Add some environment salt,
export RDBASE=/opt/RDKit_20XX_XX_X export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH
Resource your .bashrc
if you want the InChI stuff (trust me you do), first:
cd $RDBASE/External/INCHI-API/ ./download-inchi.sh
Build (compile), install & test
cd $RDBASE mkdir build cd build cmake .. # if you do not care for InChI support OR cmake -DRDK_BUILD_INCHI_SUPPORT=ON .. # to install InChI generation code make # -j 4 to use multiple processors make install ctest
If all your tests passed successful you are good to go. Otherwise, get in touch via the post comments below.