Supporting Information for the paper "Deep learning enables rapid identification of potent DDR1 kinase inhibitors".
The GENTRL model is a variational autoencoder with a rich prior distribution of the latent space. We used tensor decompositions to encode the relations between molecular structures and their properties and to learn on data with missing values. We train the model in two steps. First, we learn a mapping of a chemical space on the latent manifold by maximizing the evidence lower bound. We then freeze all the parameters except for the learnable prior and explore the chemical space to find molecules with a high reward.
In this repository, we provide an implementation of a GENTRL model with an example trained on a MOSES dataset.
To run the training procedure,
- Install RDKit to process molecules
- Install GENTRL model:
python setup.py install - Install MOSES from the repository
- Run the pretrain.ipynb to train an autoencoder
- Run the train_rl.ipynb to optimize a reward function
implementation of GENTRL in Tensorflow
python setup.py install running install running bdist_egg running egg_info writing gentrl.egg-info/PKG-INFO writing dependency_links to gentrl.egg-info/dependency_links.txt writing top-level names to gentrl.egg-info/top_level.txt reading manifest file 'gentrl.egg-info/SOURCES.txt' writing manifest file 'gentrl.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py copying gentrl/encoder.py -> build/lib/gentrl copying gentrl/decoder.py -> build/lib/gentrl copying gentrl/dataloader.py -> build/lib/gentrl copying gentrl/tokenizer.py -> build/lib/gentrl copying gentrl/gentrl.py -> build/lib/gentrl copying gentrl/lp.py -> build/lib/gentrl copying gentrl/init.py -> build/lib/gentrl creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/encoder.py -> build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/decoder.py -> build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/dataloader.py -> build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/tokenizer.py -> build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/gentrl.py -> build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/lp.py -> build/bdist.linux-x86_64/egg/gentrl copying build/lib/gentrl/init.py -> build/bdist.linux-x86_64/egg/gentrl byte-compiling build/bdist.linux-x86_64/egg/gentrl/encoder.py to encoder.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/gentrl/decoder.py to decoder.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/gentrl/dataloader.py to dataloader.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/gentrl/tokenizer.py to tokenizer.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/gentrl/gentrl.py to gentrl.cpython-37.pyc File "build/bdist.linux-x86_64/egg/gentrl/gentrl.py", line 38 class GENTRL(tf.Module) ^ SyntaxError: invalid syntax
byte-compiling build/bdist.linux-x86_64/egg/gentrl/lp.py to lp.cpython-37.pyc byte-compiling build/bdist.linux-x86_64/egg/gentrl/init.py to init.cpython-37.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying gentrl.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying gentrl.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying gentrl.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying gentrl.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating 'dist/gentrl-0.1-py3.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing gentrl-0.1-py3.7.egg Copying gentrl-0.1-py3.7.egg to /home/groups/ruthm/zyzhang/sw/sherlock2/anaconda-envs/tfGENTRL/lib/python3.7/site-packages Adding gentrl 0.1 to easy-install.pth file
Installed /home/groups/ruthm/zyzhang/sw/sherlock2/anaconda-envs/tfGENTRL/lib/python3.7/site-packages/gentrl-0.1-py3.7.egg Processing dependencies for gentrl==0.1 Finished processing dependencies for gentrl==0.1