shape-it

Description

Code for shape-it with openbabel3 and rdkit

INSTALL

• Following example is the basic way to install the tool:

git clone https://github.com/rdkit/shape-it.git
cd shape-it
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=<where you want to install> ..
make
make install

• If you would like to use rdkit for shape-it please set BUILD_RDKIT_SUPPORT=ON. Also set BUILD_PYTHON_SUPPORT=ON, you can call shape-it as a library:

cd shape-it
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=<where you want to install> -DBUILD_RDKIT_SUPPORT=ON -DBUILD_PYTHON_SUPPORT=ON ..
make
make install

Tips

• If the make command failed, you should try to set RDKIT_INCLUDE_DIR, Boost_INCLUDE_DIR option.

cmake -DCMAKE_INSTALL_PREFIX=/home/iwatobipen/src/shape-it -DRDKIT_INCLUDE_DIR=/home/iwatobipen/miniconda3/envs/chemoinfo/include/rdkit -DBUILD_RDKIT_SUPPORT=ON -DBUILD_PYTHON_SUPPORT=ON -DBoost_INCLUDE_DIR=/home/iwatobipen/miniconda3/envs/chemoinfo/pkgs/libboost-1.73.0-hf484d3e_11/include ..
make
make install

Original code and basic usage

• http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html

History of shape-it and how to cite

Shape-it is a shape-only rewrite of the original Pharao code that was developed in 2008 by Silicos (Jonatan Taminau, Gert Thijs and Hans De Winter). It is based on the alignment method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503). If you use this code in your research, we would appreciate if you would include the following citation in your publication:

Taminau, J.; Thijs, G.; De Winter, H. (2008) ‘Pharao: Pharmacophore alignment and optimization’, J. Mol. Graph. Model. 2008, 27, 161-169