.
├── crawling
│ ├── download_ligand_sdf.py
│ ├── download_ligand_smi.py
│ ├── download_protein.py
│ ├── find_ligand_of_pdb.py
│ ├── get_ligand_set.py
│ └── README.md
├── docking
│ ├── docking.py
│ └── split_sdf.py
├── LICENSE
├── preprocess
│ └── preprocess.py
├── README.md
├── similarity
│ ├── ligand
│ │ ├── cat_fps.py
│ │ ├── extract_valids.py
│ │ ├── generate_fps.py
│ │ ├── gpu_similarity.py
│ │ └── README.md
│ └── protein_clustering
│ ├── clustering.sh
│ ├── filter.py
│ ├── parser.py
│ ├── pdb2fasta.py
│ ├── README.md
│ └── target_list.py
└── transformation
├── check_rmsd.py
├── dihedral.py
├── rotation.py
└── translation.py- crawling
Crawling SMILES, PDB, SDF and etc from the rcsb pdb or pdbbind. - docking
Scripts for docking with SMINA. - preprocess
Preprocess code for docked data. - similarity
- Ligand
Small molecules filtering based on the Tanimoto Similarity. - Protein
Protein filtering based on the cd-hit.
- transformation
Code for tranform the molecule conformation.