scripts/preprocess_dataset.json

{
"PARSE_PROTEIN": 1,
"PARSE_DNA": 1,
"PARSE_RNA": 1,
"PARSE_RNA_AS_DNA": 0,
"NA_SHARED_TOKENS": 1,
"NA_REF_ATOM": "C1'",
"INCLUDE_PRED_NA_N": 1,
"PROTEIN_BACKBONE_OCC_CUTOFF" : 0.8,
"PROTEIN_SIDE_CHAIN_OCC_CUTOFF": 0.5,
"DNA_BACKBONE_OCC_CUTOFF" : 0.8,
"DNA_SIDE_CHAIN_OCC_CUTOFF": 0.5,
"RNA_BACKBONE_OCC_CUTOFF" : 0.8,
"RNA_SIDE_CHAIN_OCC_CUTOFF": 0.5,
"LIGAND_OCC_CUTOFF": 0.01,
"BATCH_TOKENS" : 6000,
"EXCLUDE_RES" : ["HOH", "NA", "CL", "K", "BR"],
"RANDOMIZE_NMR_MODEL" : 0,
"CROP_LARGE_STRUCTURES" : 0,
"MIN_OVERLAP_LENGTH": 5,
"NUM_NEIGHBORS": 48,
"ATOMS_TO_LOAD" : "all"
}