├── .gitignore ├── LICENSE ├── README.md ├── dataset └── Ago │ ├── AGO_050_model_3_ptm.pdb │ ├── Ago.fix.txt │ ├── Ago_database.csv │ ├── pfago.conserve.fix.txt │ └── pfago.piwi.fix.txt ├── environment.yaml ├── img └── framework.png ├── protein_DIFF ├── MSA_Transition_Matrix.py ├── dataset │ ├── __init__.py │ ├── a2m_to_pdb.py │ ├── blosum_substitute.pt │ ├── cath_2nd.py │ ├── cath_imem_2nd.py │ ├── compute_confidence.py │ ├── generate_MSA_graph.py │ ├── generate_graph.py │ ├── large_dataset.py │ ├── pdbbind_eval.py │ ├── pdbbind_eval_multi.py │ ├── predict_structure.py │ ├── repair_pdb.py │ ├── secondary_structure.py │ ├── select_residual_from_pdb.py │ └── utils.py ├── dgd │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── utils.cpython-310.pyc │ │ └── utils.cpython-39.pyc │ ├── analysis │ │ ├── __init__.py │ │ ├── dist_helper.py │ │ ├── orca │ │ │ ├── orca.cpp │ │ │ └── orca.h │ │ ├── rdkit_functions.py │ │ ├── spectre_utils.py │ │ └── visualization.py │ ├── datasets │ │ ├── __init__.py │ │ ├── abstract_dataset.py │ │ ├── cath_imem_2nd.py │ │ ├── qm9_dataset.py │ │ ├── spectre_dataset.py │ │ └── utils.py │ ├── diffusion │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-310.pyc │ │ │ ├── diffusion_utils.cpython-310.pyc │ │ │ └── noise_schedule.cpython-310.pyc │ │ ├── diffusion_utils.py │ │ ├── distributions.py │ │ ├── extra_features.py │ │ ├── extra_features_molecular.py │ │ ├── layers.py │ │ └── noise_schedule.py │ ├── main.py │ ├── metrics │ │ ├── __init__.py │ │ ├── abstract_metrics.py │ │ ├── molecular_metrics.py │ │ ├── molecular_metrics_discrete.py │ │ └── train_metrics.py │ ├── models │ │ ├── __init__.py │ │ ├── layers.py │ │ └── transformer_model.py │ └── utils.py ├── inference.py ├── model │ └── egnn_pytorch │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── egnn_pyg_v2.cpython-310.pyc │ │ ├── egnn_pytorch.cpython-310.pyc │ │ └── utils.cpython-310.pyc │ │ ├── egnn_pyg_v0.py │ │ ├── egnn_pyg_v2.py │ │ ├── egnn_pytorch.py │ │ ├── egnn_pytorch_geometric.py │ │ ├── untitled.txt │ │ └── utils.py ├── run_pt.py ├── utils.py └── utils │ └── utils.py └── script ├── gen_graph.sh └── inference.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/README.md -------------------------------------------------------------------------------- /dataset/Ago/AGO_050_model_3_ptm.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/dataset/Ago/AGO_050_model_3_ptm.pdb -------------------------------------------------------------------------------- /dataset/Ago/Ago.fix.txt: -------------------------------------------------------------------------------- 1 | D713 -------------------------------------------------------------------------------- /dataset/Ago/Ago_database.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/dataset/Ago/Ago_database.csv -------------------------------------------------------------------------------- /dataset/Ago/pfago.conserve.fix.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/dataset/Ago/pfago.conserve.fix.txt -------------------------------------------------------------------------------- /dataset/Ago/pfago.piwi.fix.txt: -------------------------------------------------------------------------------- 1 | D558 2 | E596 3 | D628 4 | H745 -------------------------------------------------------------------------------- /environment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/environment.yaml -------------------------------------------------------------------------------- /img/framework.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/img/framework.png -------------------------------------------------------------------------------- /protein_DIFF/MSA_Transition_Matrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/MSA_Transition_Matrix.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dataset/a2m_to_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/a2m_to_pdb.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/blosum_substitute.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/blosum_substitute.pt -------------------------------------------------------------------------------- /protein_DIFF/dataset/cath_2nd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/cath_2nd.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/cath_imem_2nd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/cath_imem_2nd.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/compute_confidence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/compute_confidence.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/generate_MSA_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/generate_MSA_graph.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/generate_graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/generate_graph.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/large_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/large_dataset.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/pdbbind_eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/pdbbind_eval.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/pdbbind_eval_multi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/pdbbind_eval_multi.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/predict_structure.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/predict_structure.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/repair_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/repair_pdb.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/secondary_structure.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/secondary_structure.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/select_residual_from_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/select_residual_from_pdb.py -------------------------------------------------------------------------------- /protein_DIFF/dataset/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dataset/utils.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/__pycache__/__init__.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/__pycache__/__init__.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/dgd/__pycache__/__init__.cpython-39.pyc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/__pycache__/utils.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/__pycache__/utils.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/dgd/__pycache__/utils.cpython-39.pyc: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/dist_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/analysis/dist_helper.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/orca/orca.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/analysis/orca/orca.cpp -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/orca/orca.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/analysis/orca/orca.h -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/rdkit_functions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/analysis/rdkit_functions.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/spectre_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/analysis/spectre_utils.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/analysis/visualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/analysis/visualization.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/datasets/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/datasets/abstract_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/datasets/abstract_dataset.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/datasets/cath_imem_2nd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/datasets/cath_imem_2nd.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/datasets/qm9_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/datasets/qm9_dataset.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/datasets/spectre_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/datasets/spectre_dataset.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/datasets/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/datasets/utils.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/__pycache__/__init__.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/__pycache__/__init__.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/__pycache__/diffusion_utils.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/__pycache__/diffusion_utils.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/__pycache__/noise_schedule.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/__pycache__/noise_schedule.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/diffusion_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/diffusion_utils.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/distributions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/distributions.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/extra_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/extra_features.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/extra_features_molecular.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/extra_features_molecular.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/layers.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/diffusion/noise_schedule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/diffusion/noise_schedule.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/main.py -------------------------------------------------------------------------------- /protein_DIFF/dgd/metrics/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/metrics/abstract_metrics.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/metrics/molecular_metrics.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/metrics/molecular_metrics_discrete.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/metrics/train_metrics.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/models/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/models/layers.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/models/transformer_model.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/dgd/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/dgd/utils.py -------------------------------------------------------------------------------- /protein_DIFF/inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/inference.py -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/__init__.py -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/__pycache__/__init__.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/__pycache__/__init__.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/__pycache__/egnn_pyg_v2.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/__pycache__/egnn_pyg_v2.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/__pycache__/egnn_pytorch.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/__pycache__/egnn_pytorch.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/__pycache__/utils.cpython-310.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/__pycache__/utils.cpython-310.pyc -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/egnn_pyg_v0.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/egnn_pyg_v0.py -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/egnn_pyg_v2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/egnn_pyg_v2.py -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/egnn_pytorch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/egnn_pytorch.py -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/egnn_pytorch_geometric.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/egnn_pytorch_geometric.py -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/untitled.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /protein_DIFF/model/egnn_pytorch/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/model/egnn_pytorch/utils.py -------------------------------------------------------------------------------- /protein_DIFF/run_pt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/run_pt.py -------------------------------------------------------------------------------- /protein_DIFF/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/utils.py -------------------------------------------------------------------------------- /protein_DIFF/utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/protein_DIFF/utils/utils.py -------------------------------------------------------------------------------- /script/gen_graph.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/script/gen_graph.sh -------------------------------------------------------------------------------- /script/inference.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bzho3923/CPDiffusion/HEAD/script/inference.sh --------------------------------------------------------------------------------