├── .gitignore ├── LICENSE ├── README.md ├── assets ├── compare.png ├── initial.png ├── reproduce.png ├── toc.png ├── ubuntu18.png └── ubuntu20.png ├── configs ├── sample.yml ├── train_frag.yml ├── train_frag_continue.yml ├── train_frag_moad.yml ├── train_frag_moad_on_cross.yml ├── train_linker.yml ├── train_linker_continue.yml ├── train_linker_moad.yml ├── train_linker_moad_oncross.yml ├── train_scaffold.yml ├── train_scaffold_moad.yml ├── train_scaffold_moad_oncross.yml ├── train_side_chain.yml ├── train_side_chain_moad.yml └── train_side_chain_moad_oncross.yml ├── data ├── 3cl.pdb ├── 3cl_ligand.sdf ├── 3cl_ligand_H.sdf └── surface_maker_test.py ├── delete.py ├── delete_environment.yml ├── delete_train.py ├── evaluation ├── README.md └── shape_score.py ├── example ├── Eg5 │ ├── 3zcw_2_pocket_8.0_res_1.5.ply │ ├── 3zcw_frag.sdf │ ├── 3zcw_ligand.sdf │ └── 3zcw_protein.pdb ├── IMDPH │ ├── 5OU3_fragment.sdf │ ├── 5OU3_ligand.mol2 │ ├── 5OU3_pocket_8.0.ply │ └── 5OU3_protein.pdb ├── adrb1 │ ├── 2VT4_frag.sdf │ ├── 2VT4_ligand.sdf │ ├── 2VT4_protein.pdb │ └── adrb_pocket_8.0.ply ├── drd2 │ ├── 6CM4_frag.sdf │ ├── 6CM4_ligand.sdf │ ├── 6CM4_protein.pdb │ └── drd2_pocket_8.0.ply └── smarca2 │ ├── 6HAX_frag.sdf │ ├── 6HAX_ligand.sdf │ ├── 6HAX_protein.pdb │ └── smarca2_pocket_8.0.ply ├── gen_all_epoch_to_1_target.py ├── install_software └── README.md ├── models ├── delete.py ├── embedding.py ├── generation │ ├── __init__.py │ ├── attachment.py │ ├── geometry.py │ └── topology.py ├── interaction │ ├── __init__.py │ └── interaction.py ├── invariant.py ├── model_utils.py └── sample.py ├── process_your_data.py ├── surf_maker_environment.yml └── utils ├── chem.py ├── data.py ├── datasets ├── __init__.py ├── ligand.py ├── pl.py └── surfdata.py ├── linker.py ├── masif ├── __init_.py ├── chemistry.py ├── computeAPBS.py ├── computeCharges.py ├── computeHydrophobicity.py ├── computeMSMS.py ├── compute_normal.py ├── fixmesh.py ├── generate_prot_ply.py └── save_ply.py ├── misc.py ├── pdb_parser.py ├── protein_ligand copy.py ├── protein_ligand.py ├── reconstruct.py ├── sample.py ├── surface.py ├── train.py ├── transforms copy.py └── transforms.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OdinZhang/Delete/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OdinZhang/Delete/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/OdinZhang/Delete/HEAD/README.md -------------------------------------------------------------------------------- /assets/compare.png: -------------------------------------------------------------------------------- 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