NA-MPNN/design_model.json at main · baker-laboratory/NA-MPNN · GitHub

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{
"VOCAB_SIZE": 33,
"NUM_LETTERS": 33,
"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,
"EXCLUDED_ELEMENTS": [1],
"DATE_CUTOFF" : "2030-01-01",
"MAX_NUMBER_OF_PDBS_TRAIN" : 20000,
"MAX_NUMBER_OF_PDBS_VALID" : 200,
"BATCH_TOKENS" : 6000,
"LOSS_TOKENS" : 6000,
"LABEL_SMOOTHING": 0.1,
"EXCLUDE_RES" : ["HOH", "NA", "CL", "K", "BR"],
"MIN_PROTEIN_LENGTH_CUTOFF" : 1,
"NUM_WORKERS" : 12,
"TOTAL_STEPS" : 100000,
"RANDOMIZE_NMR_MODEL" : 0,
"CROP_LARGE_STRUCTURES" : 0,
"MIN_OVERLAP_LENGTH": 5,
"DF_PATH_TRAIN" : "/home/akubaney/projects/na_mpnn/data/datasets/design_dataset_v2/train.csv",
"DF_PATH_VALID" : "/home/akubaney/projects/na_mpnn/data/datasets/design_dataset_v2/valid.csv",
"BASE_FOLDER" : "/home/akubaney/projects/na_mpnn/models/design_model",
"PREV_CHECKPOINT" : "/home/akubaney/projects/na_mpnn/models/design_model/last.pt",
"HIDDEN_DIM" : 128,
"NUM_ENCODER_LAYERS" : 3,
"NUM_DECODER_LAYERS" : 3,
"NUM_NEIGHBORS": 32,
"DROPOUT": 0.1,
"DECODE_PROTEIN_FIRST": 0,
"PROTEIN_BACKBONE_NOISE" : 0.1,
"DNA_BACKBONE_NOISE" : 0.1,
"RNA_BACKBONE_NOISE": 0.1,
"PARSE_PPMS": 0,
"NA_ONLY_AS_UNIFORM_PPM": 0,
"DROP_PROTEIN_PROBABILITY": 0,
"PROTEIN_INTERFACE_RESIDUE_MUTATION_PROBABILITY": 0,
"MUTATE_BASE_PAIR_TOGETHER": 0,
"MUTATE_ENTIRE_SIDE_CHAIN_INTERFACE_PROBABILITY": 0,
"NA_NON_INTERFACE_AS_UNIFORM_PPM": 0,
"GRADIENT_NORM" : 1.0,
"MIXED_PRECISION": 1,
"SAVE_EVERY_N_STEPS": 1000,
"ATOMS_TO_LOAD" : "backbone",
"METRICS_TO_COMPUTE": "basic"
}