├── Arguments.py ├── LICENSE ├── README.md ├── benchmark_layers.py ├── benchmark_models.py ├── benchmark_scripts ├── DGCNN_site.sh ├── Pointnet_site.sh ├── dMaSIF_search.sh └── dMaSIF_site.sh ├── dMaSIF_Colab_V1.ipynb ├── data.py ├── data_analysis ├── analyse_atomnet.ipynb ├── analyse_descriptors.py ├── analyse_descriptors_para.py ├── analyse_output.ipynb ├── analyse_site_outputs.py ├── analyse_site_outputs_graph.ipynb ├── plot_search.ipynb └── profiling_surface.ipynb ├── data_iteration.py ├── data_preprocessing ├── __pycache__ │ ├── convert_pdb2npy.cpython-37.pyc │ ├── convert_ply2npy.cpython-37.pyc │ └── download_pdb.cpython-37.pyc ├── convert_pdb2npy.py ├── convert_ply2npy.py └── download_pdb.py ├── example ├── complexexample.pdb └── monomerexample.pdb ├── geometry_processing.py ├── helper.py ├── lists ├── testing.txt ├── testing_ppi.txt ├── training.txt └── training_ppi.txt ├── main_inference.py ├── main_training.py ├── model.py ├── models ├── dMaSIF_search_3layer_12A_16dim ├── dMaSIF_site_3layer_16dims_12A_0.7res_150sup_epoch59 ├── dMaSIF_site_3layer_16dims_12A_100sup_epoch71 ├── dMaSIF_site_3layer_16dims_9A_0.7res_150sup_epoch85 └── dMaSIF_site_3layer_16dims_9A_100sup_epoch64 └── overview.PNG /Arguments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/casperg92/MaSIF_colab/HEAD/Arguments.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/casperg92/MaSIF_colab/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/casperg92/MaSIF_colab/HEAD/README.md -------------------------------------------------------------------------------- /benchmark_layers.py: 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