├── .gitignore ├── README.md ├── config.py ├── data ├── __init__.py ├── count_substructures.py ├── data.py ├── data_ood.py ├── data_oversquashing.py ├── fragmentations │ ├── bbb │ │ └── breaking_bridge_bonds.py │ ├── fragmentations.py │ ├── magnet │ │ └── magnet.py │ └── psm │ │ ├── mol_bpe.py │ │ ├── molecule.py │ │ └── utils │ │ ├── __init__.py │ │ ├── chem_utils.py │ │ └── logger.py ├── graph_to_mol.py ├── lrgb │ └── lrgb.py └── plogp.py ├── environment.yml ├── experiment ├── ZINC_10k.yaml ├── ZINC_full.yaml ├── ZINC_full_cosine.yaml ├── peptides_func.yaml └── peptides_struct.yaml ├── main_experiment.py └── models ├── fragGNN.py ├── gcn.py ├── layers.py └── lightning_models.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/README.md -------------------------------------------------------------------------------- /config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/config.py -------------------------------------------------------------------------------- /data/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/count_substructures.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/count_substructures.py -------------------------------------------------------------------------------- /data/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/data.py -------------------------------------------------------------------------------- /data/data_ood.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/data_ood.py -------------------------------------------------------------------------------- /data/data_oversquashing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/data_oversquashing.py -------------------------------------------------------------------------------- /data/fragmentations/bbb/breaking_bridge_bonds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/fragmentations/bbb/breaking_bridge_bonds.py -------------------------------------------------------------------------------- /data/fragmentations/fragmentations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/fragmentations/fragmentations.py -------------------------------------------------------------------------------- /data/fragmentations/magnet/magnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/fragmentations/magnet/magnet.py -------------------------------------------------------------------------------- /data/fragmentations/psm/mol_bpe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/fragmentations/psm/mol_bpe.py -------------------------------------------------------------------------------- /data/fragmentations/psm/molecule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KemperNiklas/FragNet/HEAD/data/fragmentations/psm/molecule.py -------------------------------------------------------------------------------- /data/fragmentations/psm/utils/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | # 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