├── ._notes ├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── config ├── runtime │ ├── andrew_test.yaml │ └── hologram_gather.yaml └── static.yaml ├── data └── CG_matrix_l=13.npy ├── env.yml ├── protein_holography ├── __init__.py ├── config.py ├── config_sampler.py ├── coordinates │ ├── COA_ref_frame.py │ ├── README.md │ ├── __init__.py │ ├── get_amino_acids.py │ ├── get_holograms.py │ ├── get_neighborhoods.py │ ├── get_structural_info.py │ ├── get_zernikegrams.py │ ├── make_pdb_list.py │ ├── preprocessor_hdf5_neighborhoods.py │ ├── preprocessor_hdf5_proteins.py │ ├── preprocessor_pdbs.py │ ├── pyrosetta_hdf5_amino_acids.py │ ├── pyrosetta_hdf5_holograms.py │ ├── pyrosetta_hdf5_neighborhoods.py │ ├── pyrosetta_hdf5_proteins.py │ └── pyrosetta_hdf5_zernikegrams.py ├── fourier │ ├── __init__.py │ ├── get_coeffs.py │ ├── hologram.py │ ├── naming.py │ ├── preprocessor.py │ ├── preprocessor2.py │ └── project.py ├── hologram │ ├── #scriptmaker.py# │ ├── __init__.py │ ├── geo.py │ ├── get_sample.py │ ├── hologram.py │ ├── pdb_interface.py │ ├── protein_dir_parse.py │ ├── sample_protein.py │ ├── scriptmaker.py │ └── test_script.py ├── model_weights │ └── README.md ├── network │ ├── L_batch_norm.py │ ├── L_batch_norm_gpu.py │ ├── __init__.py │ ├── batch_norm.py │ ├── checkpoint │ ├── clebsch.py │ ├── clebsch_saver.py │ ├── config.py │ ├── dataset.py │ ├── equivariance_test.py │ ├── hgram_test.py │ ├── hnn.py │ ├── hnn_gpu.py │ ├── hnn_intermediate.py │ ├── intermediate_output.py │ ├── linearity.py │ ├── load_test.py │ ├── naming.py │ ├── network_loader.py │ ├── nonlinearity.py │ ├── predict.py │ ├── predict_ss.py │ ├── rotation_test.py │ ├── scriptmaker.py │ ├── spherical_batch_norm.py │ ├── spherical_batch_norm_gpu.py │ ├── test.py │ ├── test.sh │ ├── test_batch_norm.py │ ├── test_plot.py │ ├── test_spherical_batch_norm.py │ ├── test_zernike.py │ ├── train.py │ ├── train_delta.py │ ├── train_gpu.py │ ├── train_gpu_generator.py │ ├── train_gpu_generator_uchenna.py │ ├── train_ss.py │ ├── train_zernike.py │ ├── vae.py │ └── wigner.py ├── predict │ ├── __init__.py │ ├── predict.py │ └── prediction_parser.py ├── preprocess │ ├── README │ ├── __init__.py │ ├── filter │ │ └── protein_selection.py │ ├── metadata │ │ └── pdb_metadata.py │ ├── pdb_list │ │ └── protein_list.py │ ├── sample │ │ ├── preprocessor.py │ │ ├── sample_all.py │ │ ├── sample_functions.py │ │ └── sample_neighborhoods.py │ └── split │ │ └── train_test_split.py ├── publication │ ├── README.md │ ├── UMAP_colored_by_aa.html │ └── UMAP_colored_by_cluster.html ├── submit.py ├── submit_sampler.py └── utils │ ├── CG_matrix_l=13.npy │ ├── __init__.py │ ├── download_model_weights.py │ ├── geo.py │ ├── get_CAs.py │ ├── posterity.py │ ├── protein.py │ ├── pyrosetta_utils.py │ └── zernikegram.py ├── scripts ├── README.md ├── process_pdbs.sh └── quick_run │ ├── pdbs.csv │ └── pdbs │ ├── 1pga.pdb │ ├── 2lzm.pdb │ └── 6m0j.pdb ├── setup.py ├── tests ├── coordinates │ ├── 1PGA.pdb │ ├── proteinG_neighborhoods.hdf5 │ ├── proteinG_structural_info.hdf5 │ ├── proteinG_zernikegrams.hdf5 │ ├── test_coordinates.py │ └── test_coordinates_module.sh └── parallel_test │ ├── 1PGA.pdb │ ├── parallel_proteinG_pdbs.hdf5 │ ├── parallel_proteinG_true_neighborhoods.hdf5 │ ├── parallel_proteinG_true_proteins.hdf5 │ ├── parallel_proteinG_true_zernikegrams.hdf5 │ └── test_parallel_coordinates.py └── tutorials ├── Network.ipynb ├── Zernike projection.ipynb ├── test └── toy_aminoacid_tutorial.ipynb /._notes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/StatPhysBio/protein_holography/HEAD/._notes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/StatPhysBio/protein_holography/HEAD/.gitignore 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