promptbind.data package

Submodules

promptbind.data.data module

class promptbind.data.data.FABindDataSet(root, data=None, protein_dict=None, compound_dict=None, proteinMode=0, compoundMode=1, add_noise_to_com=None, pocket_radius=20, contactCutoff=8.0, predDis=True, args=None, use_whole_protein=False, compound_coords_init_mode=None, seed=42, pre=None, transform=None, pre_transform=None, pre_filter=None, noise_for_predicted_pocket=5.0, test_random_rotation=False, pocket_idx_no_noise=True, use_esm2_feat=False)

Bases: Dataset

get(idx)

Gets the data object at index idx.

len()

Returns the number of data objects stored in the dataset.

property processed_file_names

The name of the files in the self.processed_dir folder that must be present in order to skip processing.

promptbind.data.data.get_data(args, logger, addNoise=None, use_whole_protein=False, compound_coords_init_mode='pocket_center_rdkit', pre='/PDBbind_data/pdbbind2020')

promptbind.data.inference_preprocess_mol_confs module

promptbind.data.inference_preprocess_mol_confs.get_mol_info(idx)

promptbind.data.inference_preprocess_protein module

Module contents