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OOMMPPAA / MacOSX

Setting up OOMMPPAA on MacOSX 10.8.5

You will require a functioning version of XCode 5.+

https://developer.apple.com/xcode/

install homebrew

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

install pip

sudo easy_install pip

then use pip and homebrew to do the rest

First install matplotlib

brew install freetype
brew install libpng
brew install ffmpeg
# Add more brew formulae so we can install our py libs with brew
brew tap samueljohn/python
brew tap homebrew/science
brew install numpy
brew install scipy
brew install matplotlib

Then install python modules

sudo pip install nose pyparsing ipython Django==1.5.0 tornado psycopg2 pillow gunicorn django-jfu matplotlib

Now lets make the RDKit

mkdir ~/RDKit
cd ~/RDKit
git clone https://github.com/rdkit/rdkit.git
cd rdkit

Now we want to build on this release of the RDKit.

git checkout dad1e1db5b0045e11972d931a8701c52ea90bb43

Then go into bashrc file

vim ~/.bashrc

and add:

export RDBASE=~/RDKit/rdkit
export PYTHONPATH=$RDBASE/lib:$RDBASE:PYTHONPATH
export DYLD_LIBRARY_PATH=$RDBASE/lib:$DYLD_LIBRARY_PATH

Now open a new shell and make the RDKit:

source ~/.bashrc
cd $RDBASE
mkdir build
cd build
cmake ..
make
make install

This should have worked. If it hasn't then many helpful suggestions can be found here.

You will also need INCHI support, which is compiled seperately.

cd $RDBASE/External/INCHI-API
bash download-inchi.sh
cd $RDBASE/build
cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
make
make install

Again this should complete without error.

Install pkg-config

brew install pkg-config

install openbabel

brew install open-babel

should be found in /usr/local/bin/babel. If it's not, sym-link it too that file so OOMMPPAA can find it.

Now lets get the OOMMPPAA code:

cd ~/
git clone https://abradley@bitbucket.org/abradley/oommppaa.git CHOC

Finally pull down the current database

wget https://bitbucket.org/abradley/oommppaa/downloads/OOMMPPAA_db.db ~/CHOC/src/WebApp/data/OOMMPPAA_db.db

At this point you can use Tornado as a server. Simply type:

cd ~/CHOC/src/WebApp/
python runtornado.py --port 9001 --address 127.0.0.1

Open a browser and load up 127.0.0.1:9001 and you have a working version of OOMMPPAA.

Updated