libmolgrid is a library to generate tensors from molecular data, with properties that make its output particularly suited to machine learning.
libmolgrid abstracts basic input generation functionality used in our related project, gnina, with applications reported in several papers including Protein-Ligand Scoring with Convolutional Neural Networks.
It’s implemented in C++/CUDA with Python bindings, with first-class integration for PyTorch, Caffe, and Keras.
pip install molgrid
Alternatively, you can build from source:
pip3 install numpy pytest pyquaternion
Install OpenBabel 3.0 (Not yet released, build from master).
git clone https://github.com/gnina/libmolgrid.git cd libmolgrid mkdir build cd build cmake .. make -j8 sudo make install