├── .gitignore ├── README.md ├── protein_learning ├── assessment │ ├── metrics.py │ ├── model_eval │ │ ├── model_evaluator.py │ │ └── stats_handler.py │ └── sidechain.py ├── common │ ├── data │ │ ├── README.md │ │ ├── data_types │ │ │ ├── README.md │ │ │ ├── model_input.py │ │ │ ├── model_loss.py │ │ │ ├── model_output.py │ │ │ ├── protein.py │ │ │ └── test │ │ │ │ └── test_protein.py │ │ ├── datasets │ │ │ ├── ab_dataset.py │ │ │ ├── dataset.py │ │ │ ├── protein_dataset.py │ │ │ └── utils.py │ │ └── utils.py │ ├── global_config.py │ ├── global_constants.py │ ├── helpers.py │ ├── io │ │ ├── dssp_utils.py │ │ ├── extract_cdrs.py │ │ ├── pdb_io.py │ │ ├── pdb_utils.py │ │ ├── select_atoms.py │ │ ├── sequence_utils.py │ │ └── utils.py │ ├── protein_constants.py │ ├── rigids.py │ └── transforms.py ├── examples │ ├── .ipynb_checkpoints │ │ ├── Inference-Copy1-checkpoint.ipynb │ │ ├── Inference-checkpoint.ipynb │ │ └── Sampling-checkpoint.ipynb │ ├── Inference.ipynb │ ├── Sampling.ipynb │ ├── attnpacker_inference │ │ └── examples │ │ │ ├── T0967_all_arg_pp.pdb │ │ │ ├── T0967_packed.pdb │ │ │ ├── T0967_packed_pp.pdb │ │ │ ├── T0968s2_packed.pdb │ │ │ ├── T0968s2_packed_pp.pdb │ │ │ ├── T0985_packed.pdb │ │ │ ├── T0985_packed_pp.pdb │ │ │ ├── T1043_packed.pdb │ │ │ ├── T1043_packed_pp.pdb │ │ │ ├── T1080_packed.pdb │ │ │ └── T1080_packed_pp.pdb │ ├── pdbs │ │ ├── T0967.pdb │ │ ├── T0968s2.pdb │ │ ├── T0985.pdb │ │ ├── T1043-predicted.pdb │ │ ├── T1043.pdb │ │ ├── T1057-predicted.pdb │ │ ├── T1080.pdb │ │ ├── post-processed-T0967.pdb │ │ ├── post-processed-T1043-predicted.pdb │ │ ├── post-processed-T1057-predicted.pdb │ │ └── post-processed-T1080-predicted.pdb │ ├── post_process.py │ └── statistics_example.ipynb ├── features │ ├── README.md │ ├── constants.py │ ├── default_feature_generator.py │ ├── feature.py │ ├── feature_config.py │ ├── feature_generator.py │ ├── feature_utils.py │ ├── input_embedding.py │ ├── input_features.py │ ├── masking │ │ ├── inter_chain.py │ │ ├── intra_chain.py │ │ ├── masking_utils.py │ │ ├── partition.py │ │ └── test │ │ │ └── masking_tests.py │ └── test │ │ ├── test_config.py │ │ ├── test_config_parse.py │ │ ├── test_input_embeddiing.py │ │ └── test_masking.py ├── models │ ├── .basis_cache │ │ ├── rx11 │ │ │ ├── 0.pkl.gz │ │ │ ├── 1.pkl.gz │ │ │ ├── 2.pkl.gz │ │ │ ├── 3.pkl.gz │ │ │ ├── 4.pkl.gz │ │ │ ├── 5.pkl.gz │ │ │ ├── index.pkl │ │ │ └── mutex │ │ └── rx7 │ │ │ ├── 0.pkl.gz │ │ │ ├── 1.pkl.gz │ │ │ ├── 2.pkl.gz │ │ │ ├── 3.pkl.gz │ │ │ ├── 4.pkl.gz │ │ │ ├── 5.pkl.gz │ │ │ ├── index.pkl │ │ │ └── mutex │ ├── fbb_design │ │ ├── eval_args │ │ │ └── scp_inference_args.txt │ │ ├── fbb_model.py │ │ ├── run_args │ │ │ ├── fbb_config.txt │ │ │ └── fbb_global_config.txt │ │ ├── train.py │ │ └── train_utils.py │ ├── inference_utils.py │ ├── model_abc │ │ ├── README.md │ │ ├── protein_model.py │ │ ├── structure_model.py │ │ └── train.py │ └── utils │ │ ├── dataset_augment_fns.py │ │ ├── feature_flags.py │ │ ├── model_eval.py │ │ ├── model_io.py │ │ └── opt_parse.py ├── networks │ ├── attention │ │ ├── node_attention.py │ │ └── pair_attention.py │ ├── common │ │ ├── attention_utils.py │ │ ├── constants.py │ │ ├── equivariant │ │ │ ├── feed_forward.py │ │ │ ├── fiber_units.py │ │ │ ├── linear.py │ │ │ ├── misc.py │ │ │ ├── nonlin.py │ │ │ ├── norm.py │ │ │ └── pooling.py │ │ ├── helpers │ │ │ ├── neighbor_utils.py │ │ │ ├── rotary.py │ │ │ └── torch_utils.py │ │ ├── jit_scripts.py │ │ ├── net_utils.py │ │ ├── of_rigid_utils.py │ │ ├── of_utils.py │ │ └── utils.py │ ├── config │ │ ├── global_config.py │ │ └── net_config.py │ ├── evoformer │ │ ├── evoformer.py │ │ └── evoformer_config.py │ ├── fa_coord │ │ └── coords_from_angles.py │ ├── geometric_gt │ │ ├── geom_gt_config.py │ │ └── geometric_graph_transformer.py │ ├── invariant_point_net │ │ ├── geometric_graph_attention.py │ │ ├── invariant_point_net.py │ │ └── ipn_config.py │ ├── ipa │ │ ├── invariant_point_attention.py │ │ └── ipa_config.py │ ├── loss │ │ ├── coord_loss.py │ │ ├── loss_config.py │ │ ├── loss_fn.py │ │ ├── pair_loss.py │ │ ├── residue_loss.py │ │ ├── rosetta_loss.py │ │ ├── side_chain_loss.py │ │ ├── test_loss │ │ │ └── test_inter_chain_loss.py │ │ ├── utils.py │ │ └── violation_loss.py │ ├── se3_transformer │ │ ├── attention │ │ │ ├── se3_attention.py │ │ │ └── tfn_attention.py │ │ ├── se3_attention_config.py │ │ ├── se3_transformer.py │ │ ├── se3_transformer_config.py │ │ └── tfn_transformer.py │ └── tfn │ │ ├── repr │ │ ├── basis.py │ │ ├── cache_utils.py │ │ ├── data │ │ │ ├── J_dense.npy │ │ │ └── J_dense.pt │ │ ├── fiber.py │ │ ├── irr_repr.py │ │ └── spherical_harmonics.py │ │ ├── tfn.py │ │ ├── tfn_config.py │ │ └── tfn_prox.py ├── protein_utils │ ├── align │ │ ├── kabsch_align.py │ │ └── per_residue.py │ ├── dihedral │ │ ├── angle_utils.py │ │ └── orientation_utils.py │ └── sidechains │ │ ├── project_sidechains.py │ │ ├── sidechain_rigid_utils.py │ │ └── sidechain_utils.py └── scripts │ ├── rosetta │ ├── batch_run_fast_relax.py │ ├── batch_run_idealize_relax.py │ └── batch_run_rosetta_packer.py │ └── sidechain │ ├── batch_compute_rosetta_energy.py │ ├── batch_run_faspr.py │ ├── batch_run_rosetta_packer.py │ ├── batch_run_scwrl.py │ ├── gather_stats.py │ └── standardize_scs.py ├── requirements.txt └── scp_postprocess ├── coords_from_angles.py ├── helpers.py ├── of_rigid_utils.py ├── of_utils.py ├── project_sidechains.py ├── protein_constants.py ├── rigids.py ├── sidechain_rigid_utils.py ├── sidechain_utils.py └── transforms.py /.gitignore: -------------------------------------------------------------------------------- 1 | **/__pycache__ 2 | .vs* 3 | launch.json 4 | .DS* 5 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/README.md -------------------------------------------------------------------------------- /protein_learning/assessment/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/assessment/metrics.py -------------------------------------------------------------------------------- /protein_learning/assessment/model_eval/model_evaluator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/assessment/model_eval/model_evaluator.py -------------------------------------------------------------------------------- /protein_learning/assessment/model_eval/stats_handler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/assessment/model_eval/stats_handler.py -------------------------------------------------------------------------------- /protein_learning/assessment/sidechain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/assessment/sidechain.py -------------------------------------------------------------------------------- /protein_learning/common/data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/README.md -------------------------------------------------------------------------------- /protein_learning/common/data/data_types/README.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_learning/common/data/data_types/model_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/data_types/model_input.py -------------------------------------------------------------------------------- /protein_learning/common/data/data_types/model_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/data_types/model_loss.py -------------------------------------------------------------------------------- /protein_learning/common/data/data_types/model_output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/data_types/model_output.py -------------------------------------------------------------------------------- /protein_learning/common/data/data_types/protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/data_types/protein.py -------------------------------------------------------------------------------- /protein_learning/common/data/data_types/test/test_protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/data_types/test/test_protein.py -------------------------------------------------------------------------------- /protein_learning/common/data/datasets/ab_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/datasets/ab_dataset.py -------------------------------------------------------------------------------- /protein_learning/common/data/datasets/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/datasets/dataset.py -------------------------------------------------------------------------------- /protein_learning/common/data/datasets/protein_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/datasets/protein_dataset.py -------------------------------------------------------------------------------- /protein_learning/common/data/datasets/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/datasets/utils.py -------------------------------------------------------------------------------- /protein_learning/common/data/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/data/utils.py -------------------------------------------------------------------------------- /protein_learning/common/global_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/global_config.py -------------------------------------------------------------------------------- /protein_learning/common/global_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/global_constants.py -------------------------------------------------------------------------------- /protein_learning/common/helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/helpers.py -------------------------------------------------------------------------------- /protein_learning/common/io/dssp_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/dssp_utils.py -------------------------------------------------------------------------------- /protein_learning/common/io/extract_cdrs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/extract_cdrs.py -------------------------------------------------------------------------------- /protein_learning/common/io/pdb_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/pdb_io.py -------------------------------------------------------------------------------- /protein_learning/common/io/pdb_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/pdb_utils.py -------------------------------------------------------------------------------- /protein_learning/common/io/select_atoms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/select_atoms.py -------------------------------------------------------------------------------- /protein_learning/common/io/sequence_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/sequence_utils.py -------------------------------------------------------------------------------- /protein_learning/common/io/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/io/utils.py -------------------------------------------------------------------------------- /protein_learning/common/protein_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/protein_constants.py -------------------------------------------------------------------------------- /protein_learning/common/rigids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/rigids.py -------------------------------------------------------------------------------- /protein_learning/common/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/common/transforms.py -------------------------------------------------------------------------------- /protein_learning/examples/.ipynb_checkpoints/Inference-Copy1-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/.ipynb_checkpoints/Inference-Copy1-checkpoint.ipynb -------------------------------------------------------------------------------- /protein_learning/examples/.ipynb_checkpoints/Inference-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/.ipynb_checkpoints/Inference-checkpoint.ipynb -------------------------------------------------------------------------------- /protein_learning/examples/.ipynb_checkpoints/Sampling-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/.ipynb_checkpoints/Sampling-checkpoint.ipynb -------------------------------------------------------------------------------- /protein_learning/examples/Inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/Inference.ipynb -------------------------------------------------------------------------------- /protein_learning/examples/Sampling.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/Sampling.ipynb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0967_all_arg_pp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0967_all_arg_pp.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0967_packed.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0967_packed.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0967_packed_pp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0967_packed_pp.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0968s2_packed.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0968s2_packed.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0968s2_packed_pp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0968s2_packed_pp.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0985_packed.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0985_packed.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T0985_packed_pp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T0985_packed_pp.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T1043_packed.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T1043_packed.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T1043_packed_pp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T1043_packed_pp.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T1080_packed.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T1080_packed.pdb -------------------------------------------------------------------------------- /protein_learning/examples/attnpacker_inference/examples/T1080_packed_pp.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/attnpacker_inference/examples/T1080_packed_pp.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T0967.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T0967.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T0968s2.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T0968s2.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T0985.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T0985.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T1043-predicted.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T1043-predicted.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T1043.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T1043.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T1057-predicted.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T1057-predicted.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/T1080.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/T1080.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/post-processed-T0967.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/post-processed-T0967.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/post-processed-T1043-predicted.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/post-processed-T1043-predicted.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/post-processed-T1057-predicted.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/post-processed-T1057-predicted.pdb -------------------------------------------------------------------------------- /protein_learning/examples/pdbs/post-processed-T1080-predicted.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/pdbs/post-processed-T1080-predicted.pdb -------------------------------------------------------------------------------- /protein_learning/examples/post_process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/post_process.py -------------------------------------------------------------------------------- /protein_learning/examples/statistics_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/examples/statistics_example.ipynb -------------------------------------------------------------------------------- /protein_learning/features/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/README.md -------------------------------------------------------------------------------- /protein_learning/features/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/constants.py -------------------------------------------------------------------------------- /protein_learning/features/default_feature_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/default_feature_generator.py -------------------------------------------------------------------------------- /protein_learning/features/feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/feature.py -------------------------------------------------------------------------------- /protein_learning/features/feature_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/feature_config.py -------------------------------------------------------------------------------- /protein_learning/features/feature_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/feature_generator.py -------------------------------------------------------------------------------- /protein_learning/features/feature_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/feature_utils.py -------------------------------------------------------------------------------- /protein_learning/features/input_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/input_embedding.py -------------------------------------------------------------------------------- /protein_learning/features/input_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/input_features.py -------------------------------------------------------------------------------- /protein_learning/features/masking/inter_chain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/masking/inter_chain.py -------------------------------------------------------------------------------- /protein_learning/features/masking/intra_chain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/masking/intra_chain.py -------------------------------------------------------------------------------- /protein_learning/features/masking/masking_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/masking/masking_utils.py -------------------------------------------------------------------------------- /protein_learning/features/masking/partition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/masking/partition.py -------------------------------------------------------------------------------- /protein_learning/features/masking/test/masking_tests.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_learning/features/test/test_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/test/test_config.py -------------------------------------------------------------------------------- /protein_learning/features/test/test_config_parse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/test/test_config_parse.py -------------------------------------------------------------------------------- /protein_learning/features/test/test_input_embeddiing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/test/test_input_embeddiing.py -------------------------------------------------------------------------------- /protein_learning/features/test/test_masking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/features/test/test_masking.py -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/0.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/0.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/1.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/1.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/2.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/2.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/3.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/3.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/4.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/4.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/5.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/5.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/index.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx11/index.pkl -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx11/mutex: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/0.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/0.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/1.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/1.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/2.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/2.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/3.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/3.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/4.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/4.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/5.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/5.pkl.gz -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/index.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/.basis_cache/rx7/index.pkl -------------------------------------------------------------------------------- /protein_learning/models/.basis_cache/rx7/mutex: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_learning/models/fbb_design/eval_args/scp_inference_args.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/fbb_design/eval_args/scp_inference_args.txt -------------------------------------------------------------------------------- /protein_learning/models/fbb_design/fbb_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/fbb_design/fbb_model.py -------------------------------------------------------------------------------- /protein_learning/models/fbb_design/run_args/fbb_config.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/fbb_design/run_args/fbb_config.txt -------------------------------------------------------------------------------- /protein_learning/models/fbb_design/run_args/fbb_global_config.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/fbb_design/run_args/fbb_global_config.txt -------------------------------------------------------------------------------- /protein_learning/models/fbb_design/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/fbb_design/train.py -------------------------------------------------------------------------------- /protein_learning/models/fbb_design/train_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/fbb_design/train_utils.py -------------------------------------------------------------------------------- /protein_learning/models/inference_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/inference_utils.py -------------------------------------------------------------------------------- /protein_learning/models/model_abc/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/model_abc/README.md -------------------------------------------------------------------------------- /protein_learning/models/model_abc/protein_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/model_abc/protein_model.py -------------------------------------------------------------------------------- /protein_learning/models/model_abc/structure_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/model_abc/structure_model.py -------------------------------------------------------------------------------- /protein_learning/models/model_abc/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/model_abc/train.py -------------------------------------------------------------------------------- /protein_learning/models/utils/dataset_augment_fns.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/utils/dataset_augment_fns.py -------------------------------------------------------------------------------- /protein_learning/models/utils/feature_flags.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/utils/feature_flags.py -------------------------------------------------------------------------------- /protein_learning/models/utils/model_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/utils/model_eval.py -------------------------------------------------------------------------------- /protein_learning/models/utils/model_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/utils/model_io.py -------------------------------------------------------------------------------- /protein_learning/models/utils/opt_parse.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/models/utils/opt_parse.py -------------------------------------------------------------------------------- /protein_learning/networks/attention/node_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/attention/node_attention.py -------------------------------------------------------------------------------- /protein_learning/networks/attention/pair_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/attention/pair_attention.py -------------------------------------------------------------------------------- /protein_learning/networks/common/attention_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/attention_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/common/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/constants.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/feed_forward.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/feed_forward.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/fiber_units.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/fiber_units.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/linear.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/misc.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/nonlin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/nonlin.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/norm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/norm.py -------------------------------------------------------------------------------- /protein_learning/networks/common/equivariant/pooling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/equivariant/pooling.py -------------------------------------------------------------------------------- /protein_learning/networks/common/helpers/neighbor_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/helpers/neighbor_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/common/helpers/rotary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/helpers/rotary.py -------------------------------------------------------------------------------- /protein_learning/networks/common/helpers/torch_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/helpers/torch_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/common/jit_scripts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/jit_scripts.py -------------------------------------------------------------------------------- /protein_learning/networks/common/net_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/net_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/common/of_rigid_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/of_rigid_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/common/of_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/of_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/common/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/common/utils.py -------------------------------------------------------------------------------- /protein_learning/networks/config/global_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/config/global_config.py -------------------------------------------------------------------------------- /protein_learning/networks/config/net_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/config/net_config.py -------------------------------------------------------------------------------- /protein_learning/networks/evoformer/evoformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/evoformer/evoformer.py -------------------------------------------------------------------------------- /protein_learning/networks/evoformer/evoformer_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/evoformer/evoformer_config.py -------------------------------------------------------------------------------- /protein_learning/networks/fa_coord/coords_from_angles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/fa_coord/coords_from_angles.py -------------------------------------------------------------------------------- /protein_learning/networks/geometric_gt/geom_gt_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/geometric_gt/geom_gt_config.py -------------------------------------------------------------------------------- /protein_learning/networks/geometric_gt/geometric_graph_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/geometric_gt/geometric_graph_transformer.py -------------------------------------------------------------------------------- /protein_learning/networks/invariant_point_net/geometric_graph_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/invariant_point_net/geometric_graph_attention.py -------------------------------------------------------------------------------- /protein_learning/networks/invariant_point_net/invariant_point_net.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/invariant_point_net/invariant_point_net.py -------------------------------------------------------------------------------- /protein_learning/networks/invariant_point_net/ipn_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/invariant_point_net/ipn_config.py -------------------------------------------------------------------------------- /protein_learning/networks/ipa/invariant_point_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/ipa/invariant_point_attention.py -------------------------------------------------------------------------------- /protein_learning/networks/ipa/ipa_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/ipa/ipa_config.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/coord_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/coord_loss.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/loss_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/loss_config.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/loss_fn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/loss_fn.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/pair_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/pair_loss.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/residue_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/residue_loss.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/rosetta_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/rosetta_loss.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/side_chain_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/side_chain_loss.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/test_loss/test_inter_chain_loss.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_learning/networks/loss/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/utils.py -------------------------------------------------------------------------------- /protein_learning/networks/loss/violation_loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/loss/violation_loss.py -------------------------------------------------------------------------------- /protein_learning/networks/se3_transformer/attention/se3_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/se3_transformer/attention/se3_attention.py -------------------------------------------------------------------------------- /protein_learning/networks/se3_transformer/attention/tfn_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/se3_transformer/attention/tfn_attention.py -------------------------------------------------------------------------------- /protein_learning/networks/se3_transformer/se3_attention_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/se3_transformer/se3_attention_config.py -------------------------------------------------------------------------------- /protein_learning/networks/se3_transformer/se3_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/se3_transformer/se3_transformer.py -------------------------------------------------------------------------------- /protein_learning/networks/se3_transformer/se3_transformer_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/se3_transformer/se3_transformer_config.py -------------------------------------------------------------------------------- /protein_learning/networks/se3_transformer/tfn_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/se3_transformer/tfn_transformer.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/basis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/basis.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/cache_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/cache_utils.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/data/J_dense.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/data/J_dense.npy -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/data/J_dense.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/data/J_dense.pt -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/fiber.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/fiber.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/irr_repr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/irr_repr.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/repr/spherical_harmonics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/repr/spherical_harmonics.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/tfn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/tfn.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/tfn_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/tfn_config.py -------------------------------------------------------------------------------- /protein_learning/networks/tfn/tfn_prox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/networks/tfn/tfn_prox.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/align/kabsch_align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/align/kabsch_align.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/align/per_residue.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/align/per_residue.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/dihedral/angle_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/dihedral/angle_utils.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/dihedral/orientation_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/dihedral/orientation_utils.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/sidechains/project_sidechains.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/sidechains/project_sidechains.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/sidechains/sidechain_rigid_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/sidechains/sidechain_rigid_utils.py -------------------------------------------------------------------------------- /protein_learning/protein_utils/sidechains/sidechain_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/protein_utils/sidechains/sidechain_utils.py -------------------------------------------------------------------------------- /protein_learning/scripts/rosetta/batch_run_fast_relax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/rosetta/batch_run_fast_relax.py -------------------------------------------------------------------------------- /protein_learning/scripts/rosetta/batch_run_idealize_relax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/rosetta/batch_run_idealize_relax.py -------------------------------------------------------------------------------- /protein_learning/scripts/rosetta/batch_run_rosetta_packer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/rosetta/batch_run_rosetta_packer.py -------------------------------------------------------------------------------- /protein_learning/scripts/sidechain/batch_compute_rosetta_energy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/sidechain/batch_compute_rosetta_energy.py -------------------------------------------------------------------------------- /protein_learning/scripts/sidechain/batch_run_faspr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/sidechain/batch_run_faspr.py -------------------------------------------------------------------------------- /protein_learning/scripts/sidechain/batch_run_rosetta_packer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/sidechain/batch_run_rosetta_packer.py -------------------------------------------------------------------------------- /protein_learning/scripts/sidechain/batch_run_scwrl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/sidechain/batch_run_scwrl.py -------------------------------------------------------------------------------- /protein_learning/scripts/sidechain/gather_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/sidechain/gather_stats.py -------------------------------------------------------------------------------- /protein_learning/scripts/sidechain/standardize_scs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/protein_learning/scripts/sidechain/standardize_scs.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/requirements.txt -------------------------------------------------------------------------------- /scp_postprocess/coords_from_angles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/coords_from_angles.py -------------------------------------------------------------------------------- /scp_postprocess/helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/helpers.py -------------------------------------------------------------------------------- /scp_postprocess/of_rigid_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/of_rigid_utils.py -------------------------------------------------------------------------------- /scp_postprocess/of_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/of_utils.py -------------------------------------------------------------------------------- /scp_postprocess/project_sidechains.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/project_sidechains.py -------------------------------------------------------------------------------- /scp_postprocess/protein_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/protein_constants.py -------------------------------------------------------------------------------- /scp_postprocess/rigids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/rigids.py -------------------------------------------------------------------------------- /scp_postprocess/sidechain_rigid_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/sidechain_rigid_utils.py -------------------------------------------------------------------------------- /scp_postprocess/sidechain_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/sidechain_utils.py -------------------------------------------------------------------------------- /scp_postprocess/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MattMcPartlon/AttnPacker/HEAD/scp_postprocess/transforms.py --------------------------------------------------------------------------------