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guanjq / targetdiff

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)
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Reopening issue of not having pocket10 files for training #5

Closed BJWiley233 closed 1 year ago

BJWiley233 commented 1 year ago

I am reopening this issue https://github.com/guanjq/targetdiff/issues/3 since the data folder on github has no folder called crossdocked_v1.1_rmsd1.0_pocket10. What is supposed to be in this folder? Should it have the same folder structure as this folder that is in the github link: crossdocked_v1.1_rmsd1.0 which you get after untarring?

crossdocked_v1.1_rmsd1.0
├── 1433B_HUMAN_1_240_pep_0
│   ├── 5f74_A_rec_5f74_amp_lig_tt_docked_5.sdf
│   ├── 5f74_A_rec.pdb
│   ├── 5n10_A_rec_5f74_amp_lig_tt_min_0.sdf
│   └── 5n10_A_rec.pdb
├── 1433C_TOBAC_1_256_0
│   ├── 2o98_B_rec_2o98_fsc_lig_tt_docked_0.sdf
│   └── 2o98_B_rec.pdb
├── 1433S_HUMAN_1_233_0
│   ├── 3iqu_A_rec_3p1s_fsc_lig_tt_docked_10.sdf
│   ├── 3iqu_A_rec.pdb
│   ├── 3iqv_A_rec_3iqv_fsc_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec_3p1o_fsc_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec_3p1q_fsc_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec_3p1q_fsc_lig_tt_docked_5.sdf
│   ├── 3iqv_A_rec_3p1s_fsc_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec_3smk_cw7_lig_tt_docked_1.sdf
│   ├── 3iqv_A_rec_3smm_fja_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec_3smo_fja_lig_tt_docked_2.sdf
│   ├── 3iqv_A_rec_3smo_fja_lig_tt_min_0.sdf
│   ├── 3iqv_A_rec_3sp5_cx7_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec_4dhn_0kc_lig_tt_min_0.sdf
│   ├── 3iqv_A_rec_4fr3_0v4_lig_tt_docked_2.sdf
│   ├── 3iqv_A_rec_4jdd_fsc_lig_tt_docked_1.sdf
│   ├── 3iqv_A_rec_5mxo_fsc_lig_tt_docked_0.sdf
│   ├── 3iqv_A_rec.pdb
BJWiley233 commented 1 year ago

So this will help because the owner of the other issue didn't post the solution he/she found. Having config.data.path=./data/crossdocked_v1.1_rmsd1.0_pocket10 will make ./data/crossdocked_v1.1_rmsd1.0_pocket10_processed_final.lmdb from this code here