Molecule parametrization

This repository consists of the following projects.

• Symmetrization
• Charge-group partitioning
• Maximal common fragment identification

Dependencies

• LEMON 1.3
• Qt 5.x (only for cgp-demo)

Compilation instructions

First, LEMON 1.3 needs to be installed:

wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.tar.gz
tar xvzf lemon-1.3.tar.gz
cd lemon-1.3
cmake -DCMAKE_INSTALL_PREFIX=~/lemon
make install

Note: On Mac OS 10.9, comment out the following two lines in CMakeLists.txt before doing make install

#ADD_SUBDIRECTORY(demo) 
#ADD_SUBDIRECTORY(tools)

You can remove the LEMON sources now, i.e., rm -rf lemon-1.3.

To compile the projects:

mkdir build
cd build
cmake ..
make

In case auto-detection of LEMON fails, do

cmake -DLIBLEMON_ROOT=~/lemon ..

To compile cgp-demo:

cd src/cgp-demo
qmake
make

Running

To compute maximal common fragments in 16841.lgf and 16842.lgf with a shell size of 1 do:

cd build
./fragments -no-json -s 1 ../../../data/CGP/fragments/16841.lgf ../../../data/CGP/fragments/16842.lgf

To compute all maximal common fragments of 16841.lgf and the molecules in data/fragments/lipids:

cd build
../script/fragments.py ../data/fragments/lipids/ ../data/fragments/16841.lgf ./fragments 1

The script fragments.py takes four arguments as input: the repository directory, the input molecule itself (in LGF format for now), the path to the fragments executable and the shell size.