├── .gitignore ├── LICENSE ├── README.md ├── bo ├── gauss.py ├── gauss.pyc ├── gen_latent.py ├── print_result.py ├── run_bo.py ├── run_bo.pyc ├── sascorer.py ├── sascorer.pyc ├── sparse_gp.py ├── sparse_gp.pyc ├── sparse_gp_theano_internal.py └── sparse_gp_theano_internal.pyc ├── data ├── moses │ ├── scaff_test.txt │ ├── test.txt │ ├── train.txt │ └── vocab.txt └── zinc │ ├── all.txt │ ├── opt.all.logP-SA │ ├── opt.test.logP-SA │ ├── opt.valid.logP-SA │ ├── test.txt │ ├── train.logP-SA │ ├── train.txt │ ├── valid.txt │ └── vocab.txt ├── fast_jtnn ├── __init__.py ├── chemutils.py ├── datautils.py ├── jtmpn.py ├── jtnn_dec.py ├── jtnn_enc.py ├── jtnn_vae.py ├── mol_tree.py ├── mpn.py ├── nnutils.py └── vocab.py ├── fast_molvae ├── preprocess.py ├── sample.py └── vae_train.py ├── jtnn ├── __init__.py ├── chemutils.py ├── datautils.py ├── jtmpn.py ├── jtnn_dec.py ├── jtnn_enc.py ├── jtnn_vae.py ├── jtprop_vae.py ├── mol_tree.py ├── mpn.py └── nnutils.py ├── molopt ├── optimize.py ├── pretrain.py ├── sascorer.py ├── sascorer.pyc └── vaetrain.py ├── molvae ├── draw_nei.py ├── pretrain.py ├── reconstruct.py ├── sample.py └── vaetrain.py ├── paradigm.png └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | processed/ 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kamikaze0923/jtvae/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kamikaze0923/jtvae/HEAD/README.md -------------------------------------------------------------------------------- /bo/gauss.py: -------------------------------------------------------------------------------- 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