├── LICENSE ├── README.md ├── analysis ├── SA_Score │ ├── README.md │ ├── fpscores.pkl.gz │ └── sascorer.py ├── docking.py ├── docking_py27.py ├── metrics.py ├── molecule_builder.py └── visualization.py ├── colab └── DiffSBDD.ipynb ├── configs ├── crossdock_ca_cond.yml ├── crossdock_ca_joint.yml ├── crossdock_fullatom_cond.yml ├── crossdock_fullatom_joint.yml ├── moad_ca_cond.yml ├── moad_ca_joint.yml ├── moad_fullatom_cond.yml └── moad_fullatom_joint.yml ├── constants.py ├── data ├── moad_test.txt ├── moad_train.txt ├── moad_val.txt ├── prepare_crossdocked.py ├── timesplit_no_lig_or_rec_overlap_train ├── timesplit_no_lig_or_rec_overlap_val └── timesplit_test ├── dataset.py ├── environment.yaml ├── equivariant_diffusion ├── conditional_model.py ├── dynamics.py ├── egnn_new.py └── en_diffusion.py ├── example ├── 3rfm.pdb ├── 3rfm_B_CFF.sdf ├── 5ndu.pdb ├── 5ndu_C_8V2.sdf └── fragments.sdf ├── generate_ligands.py ├── geometry_utils.py ├── img └── overview.png ├── inpaint.py ├── lightning_modules.py ├── optimize.py ├── process_bindingmoad.py ├── process_crossdock.py ├── test.py ├── train.py └── utils.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/README.md -------------------------------------------------------------------------------- /analysis/SA_Score/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/SA_Score/README.md -------------------------------------------------------------------------------- /analysis/SA_Score/fpscores.pkl.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/SA_Score/fpscores.pkl.gz -------------------------------------------------------------------------------- /analysis/SA_Score/sascorer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/SA_Score/sascorer.py -------------------------------------------------------------------------------- /analysis/docking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/docking.py -------------------------------------------------------------------------------- /analysis/docking_py27.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/docking_py27.py -------------------------------------------------------------------------------- /analysis/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/metrics.py -------------------------------------------------------------------------------- /analysis/molecule_builder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/molecule_builder.py -------------------------------------------------------------------------------- /analysis/visualization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/analysis/visualization.py -------------------------------------------------------------------------------- /colab/DiffSBDD.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/colab/DiffSBDD.ipynb -------------------------------------------------------------------------------- /configs/crossdock_ca_cond.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/crossdock_ca_cond.yml -------------------------------------------------------------------------------- /configs/crossdock_ca_joint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/crossdock_ca_joint.yml -------------------------------------------------------------------------------- /configs/crossdock_fullatom_cond.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/crossdock_fullatom_cond.yml -------------------------------------------------------------------------------- /configs/crossdock_fullatom_joint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/crossdock_fullatom_joint.yml -------------------------------------------------------------------------------- /configs/moad_ca_cond.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/moad_ca_cond.yml -------------------------------------------------------------------------------- /configs/moad_ca_joint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/moad_ca_joint.yml -------------------------------------------------------------------------------- /configs/moad_fullatom_cond.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/moad_fullatom_cond.yml -------------------------------------------------------------------------------- /configs/moad_fullatom_joint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/configs/moad_fullatom_joint.yml -------------------------------------------------------------------------------- /constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/constants.py -------------------------------------------------------------------------------- /data/moad_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/moad_test.txt -------------------------------------------------------------------------------- /data/moad_train.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/moad_train.txt -------------------------------------------------------------------------------- /data/moad_val.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/moad_val.txt -------------------------------------------------------------------------------- /data/prepare_crossdocked.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/prepare_crossdocked.py -------------------------------------------------------------------------------- /data/timesplit_no_lig_or_rec_overlap_train: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/timesplit_no_lig_or_rec_overlap_train -------------------------------------------------------------------------------- /data/timesplit_no_lig_or_rec_overlap_val: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/timesplit_no_lig_or_rec_overlap_val -------------------------------------------------------------------------------- /data/timesplit_test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/data/timesplit_test -------------------------------------------------------------------------------- /dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/dataset.py -------------------------------------------------------------------------------- /environment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/environment.yaml -------------------------------------------------------------------------------- /equivariant_diffusion/conditional_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/equivariant_diffusion/conditional_model.py -------------------------------------------------------------------------------- /equivariant_diffusion/dynamics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/equivariant_diffusion/dynamics.py -------------------------------------------------------------------------------- /equivariant_diffusion/egnn_new.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/equivariant_diffusion/egnn_new.py -------------------------------------------------------------------------------- /equivariant_diffusion/en_diffusion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/equivariant_diffusion/en_diffusion.py -------------------------------------------------------------------------------- /example/3rfm.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/example/3rfm.pdb -------------------------------------------------------------------------------- /example/3rfm_B_CFF.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/example/3rfm_B_CFF.sdf -------------------------------------------------------------------------------- /example/5ndu.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/example/5ndu.pdb -------------------------------------------------------------------------------- /example/5ndu_C_8V2.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/example/5ndu_C_8V2.sdf -------------------------------------------------------------------------------- /example/fragments.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/example/fragments.sdf -------------------------------------------------------------------------------- /generate_ligands.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/generate_ligands.py -------------------------------------------------------------------------------- /geometry_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/geometry_utils.py -------------------------------------------------------------------------------- /img/overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/img/overview.png -------------------------------------------------------------------------------- /inpaint.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/inpaint.py -------------------------------------------------------------------------------- /lightning_modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/lightning_modules.py -------------------------------------------------------------------------------- /optimize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/optimize.py -------------------------------------------------------------------------------- /process_bindingmoad.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/process_bindingmoad.py -------------------------------------------------------------------------------- /process_crossdock.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/process_crossdock.py -------------------------------------------------------------------------------- /test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/test.py -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/train.py -------------------------------------------------------------------------------- /utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/arneschneuing/DiffSBDD/HEAD/utils.py --------------------------------------------------------------------------------