To construct the synthetic action space, RxnFlow requires the reaction template set and the building block library. We provide two reaction template set:
- We provide the 107-size reaction template set templates/real.txt from Enamine REAL synthesis protocol (Gao et al.).
- The reaction template used in this paper contains 13 uni-molecular reactions and 58 bi-molecular reactions, which is constructed by Cretu et al. The template set is available under templates/hb_edited.txt.
The Enamine building block library is available upon request at https://enamine.net/building-blocks/building-blocks-catalog. We used the "Comprehensive Catalog" released at 2024.06.10.
- Refine Building Blocks
# Enamine Comprehensive Catalog
python scripts/a_enamine_catalog_to_smi.py -b `CATALOG_SDF` -o envs/enamine_catalog.smi --cpu `CPU`
# Enamine Stock
python scripts/a_enamine_stock_to_smi.py -b `STOCK_SDF` -o envs/enamine_stock.smi --cpu `CPU`
# Custom smiles
python scripts/a_refine_smi.py -b `CUSTOM_SMI` -o envs/custom_block.smi --cpu `CPU`- Create Environment
python scripts/b_create_env.py -b `SMI-FILE` -o ./envs/`ENV` -t ./templates/real.txt --cpu `CPU`All data used in the paper can be accessed in Google Drive.
Place data at experiments/.
From https://drugdesign.unistra.fr/LIT-PCBA/
| Target | PDB ID | Center |
|---|---|---|
| ADRB2 | 4ldo | -1.96, -12.27, -48.98 |
| ALDH1 | 5l2m | 34.43, -16.88, 13.77 |
| ESR_ago | 2p15 | -35.22, 4.64, 20.78 |
| ESR_antago | 2iok | 17.85, 35.51, 52.49 |
| FEN1 | 5fv7 | -16.81, -4.80, 0.62 |
| GBA | 2v3d | 32.44, 33.88, -19.56 |
| IDH1 | 4umx | 12.11, 28.09, 80.47 |
| KAT2A | 5h86 | -0.11, 5.73, 10.14 |
| MAPK1 | 4zzn | -15.69, 14.49, 42.72 |
| MTORC1 | 4dri | 35.38, 49.65, 36.21 |
| OPRK1 | 6b73 | 58.61, -24.16, -4.32 |
| PKM2 | 4jpg | 8.64, 2.94, 10.76 |
| PPARG | 5y2t | 8.30, -1.02, 46.32 |
| TP53 | 3zme | 89.32, 91.82, -44.87 |
| VDR | 3a2i | 11.38, -3.12, -31.57 |
NOTE: There is some valence issue, we remove 2623'th Atom (O) in PPARG.
From https://github.com/gnina/models/tree/master/data/CrossDocked2020
(15,201 training pockets + 100 test pockets.)
python scripts/d_create_crossdocked_db.py