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Pharmit Dataset

⚠️ Note: December 6th 2025: We are going to uplaoad the Pharmit Dataset to a public server in a few days. Below is documentation for when it is available.

The pharmit dataset is available for independent use separate from OMTRA. The dataset class can be found under pharmit_utils/pharmit.py. An instance of the PharmitDataset class can be configured to return RDKit molecules or a dictionary of tensors.

Usage

Argument Default Description
data_dir Requires Path to Pharmit dataset Zarr store.
split Required Data split.
return_type Required Options: rdkit or dict. If rdkit, ligands are returned as RDKit molecules. Extra features and pharmacophore data will not be returned. If dict, ligand data will be returned as a dictionary of tensors. Extra features and pharmacophore data will be stored as nested dictionaries under the keys extra_feats and pharm, respectively.
include_pharmacophore False Include pharmacophore features.
include_extra_feats False Include atom extra features: implicit hydrogens, aromatic flag, hybridization, ring flag, chiral flag.
n_chunks_cache 4

Example Usage

dataset = PharmitDataset(data_dir='/net/galaxy/home/koes/icd3/moldiff/OMTRA/data/pharmit',
                         split='test',
                         return_type='rdkit')
mol = dataset[0]