├── .gitignore ├── LICENSE ├── README.md ├── analysis ├── analysis.ipynb ├── dist.pdf └── year.pdf ├── assets └── workflow.svg ├── env.yml ├── error_fix ├── HiQBind-poly.md ├── HiQBind-sm.md ├── HiQBind.md ├── PDBBind-opt-poly.md ├── PDBBind-opt-sm.md ├── PDBBind-opt.md └── report.ipynb ├── figshare ├── README.md ├── hiqbind_metadata.csv ├── hiqbind_poly_metadata.csv └── hiqbind_sm_metadata.csv ├── hiqbind ├── __init__.py ├── building_blocks.csv ├── dimorphite_dl │ ├── .gitignore │ ├── CHANGES.md │ ├── CONTRIBUTORS.md │ ├── LICENSE.txt │ ├── README.md │ ├── __init__.py │ ├── dimorphite_dl.py │ ├── sample_molecules.smi │ ├── site_substructures.smarts │ └── training_data │ │ ├── README.md │ │ └── training_data.json ├── fix_ligand.py ├── fix_polymer.py ├── fix_protein.py ├── gather.py ├── manual_smiles.json ├── process.py ├── query.txt └── rcsb.py ├── pre_process ├── create_hiqbind_input.ipynb ├── create_pdbbind_input.ipynb ├── hiq_poly.csv └── hiq_sm.csv ├── pyproject.toml └── tests ├── LLP.xml ├── LLP_top.xml ├── benzene.sdf ├── benzene_fixed.sdf ├── fix_polymer.ipynb ├── test.pdb ├── test_GSH_EAA.pdb ├── test_dl.py ├── test_fix_ligand.py ├── test_fixing_residues.ipynb └── test_parametrize_ligands.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/README.md -------------------------------------------------------------------------------- /analysis/analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/analysis/analysis.ipynb -------------------------------------------------------------------------------- /analysis/dist.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/analysis/dist.pdf -------------------------------------------------------------------------------- /analysis/year.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/analysis/year.pdf -------------------------------------------------------------------------------- /assets/workflow.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/assets/workflow.svg -------------------------------------------------------------------------------- /env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/env.yml -------------------------------------------------------------------------------- /error_fix/HiQBind-poly.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/HiQBind-poly.md -------------------------------------------------------------------------------- /error_fix/HiQBind-sm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/HiQBind-sm.md -------------------------------------------------------------------------------- /error_fix/HiQBind.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/HiQBind.md -------------------------------------------------------------------------------- /error_fix/PDBBind-opt-poly.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/PDBBind-opt-poly.md -------------------------------------------------------------------------------- /error_fix/PDBBind-opt-sm.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/PDBBind-opt-sm.md -------------------------------------------------------------------------------- /error_fix/PDBBind-opt.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/PDBBind-opt.md -------------------------------------------------------------------------------- /error_fix/report.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/error_fix/report.ipynb -------------------------------------------------------------------------------- /figshare/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/figshare/README.md -------------------------------------------------------------------------------- /figshare/hiqbind_metadata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/figshare/hiqbind_metadata.csv -------------------------------------------------------------------------------- /figshare/hiqbind_poly_metadata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/figshare/hiqbind_poly_metadata.csv -------------------------------------------------------------------------------- /figshare/hiqbind_sm_metadata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/figshare/hiqbind_sm_metadata.csv -------------------------------------------------------------------------------- /hiqbind/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/__init__.py -------------------------------------------------------------------------------- /hiqbind/building_blocks.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/building_blocks.csv -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | NOTES.txt 3 | .DS_Store 4 | .ipynb_checkpoints 5 | -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/CHANGES.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/CHANGES.md -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/CONTRIBUTORS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/CONTRIBUTORS.md -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/LICENSE.txt -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/README.md -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/__init__.py -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/dimorphite_dl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/dimorphite_dl.py -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/sample_molecules.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/sample_molecules.smi -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/site_substructures.smarts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/site_substructures.smarts -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/training_data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/training_data/README.md -------------------------------------------------------------------------------- /hiqbind/dimorphite_dl/training_data/training_data.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/dimorphite_dl/training_data/training_data.json -------------------------------------------------------------------------------- /hiqbind/fix_ligand.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/fix_ligand.py -------------------------------------------------------------------------------- /hiqbind/fix_polymer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/fix_polymer.py -------------------------------------------------------------------------------- /hiqbind/fix_protein.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/fix_protein.py -------------------------------------------------------------------------------- /hiqbind/gather.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/gather.py -------------------------------------------------------------------------------- /hiqbind/manual_smiles.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/manual_smiles.json -------------------------------------------------------------------------------- /hiqbind/process.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/process.py -------------------------------------------------------------------------------- /hiqbind/query.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/query.txt -------------------------------------------------------------------------------- /hiqbind/rcsb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/hiqbind/rcsb.py -------------------------------------------------------------------------------- /pre_process/create_hiqbind_input.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/pre_process/create_hiqbind_input.ipynb -------------------------------------------------------------------------------- /pre_process/create_pdbbind_input.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/pre_process/create_pdbbind_input.ipynb -------------------------------------------------------------------------------- /pre_process/hiq_poly.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/pre_process/hiq_poly.csv -------------------------------------------------------------------------------- /pre_process/hiq_sm.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/pre_process/hiq_sm.csv -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/pyproject.toml -------------------------------------------------------------------------------- /tests/LLP.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/LLP.xml -------------------------------------------------------------------------------- /tests/LLP_top.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/LLP_top.xml -------------------------------------------------------------------------------- /tests/benzene.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/benzene.sdf -------------------------------------------------------------------------------- /tests/benzene_fixed.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/benzene_fixed.sdf -------------------------------------------------------------------------------- /tests/fix_polymer.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/fix_polymer.ipynb -------------------------------------------------------------------------------- /tests/test.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/test.pdb -------------------------------------------------------------------------------- /tests/test_GSH_EAA.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/test_GSH_EAA.pdb -------------------------------------------------------------------------------- /tests/test_dl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/test_dl.py -------------------------------------------------------------------------------- /tests/test_fix_ligand.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/test_fix_ligand.py -------------------------------------------------------------------------------- /tests/test_fixing_residues.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/test_fixing_residues.ipynb -------------------------------------------------------------------------------- /tests/test_parametrize_ligands.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/THGLab/HiQBind/HEAD/tests/test_parametrize_ligands.py --------------------------------------------------------------------------------