import copy import ml_collections as mlc def model_config(name): c = copy.deepcopy(config) if(name == "model_3"): c.model.template.enabled = False elif(name == "model_4"): c.model.template.enabled = False elif(name == "model_5"): c.model.template.enabled = False return c c_z = mlc.FieldReference(128) c_m = mlc.FieldReference(256) c_t = mlc.FieldReference(64) c_e = mlc.FieldReference(64) c_s = mlc.FieldReference(384) blocks_per_ckpt = mlc.FieldReference(1, field_type=int) chunk_size = mlc.FieldReference(None, field_type=int) aux_distogram_bins = mlc.FieldReference(64) eps = 1e-4 inf = 1e4 config = mlc.ConfigDict({ "model": { "c_z": c_z, "c_m": c_m, "c_t": c_t, "c_e": c_e, "c_s": c_s, "no_cycles": 4, "_mask_trans": False, "input_embedder": { "tf_dim": 22, "msa_dim": 49, "c_z": c_z, "c_m": c_m, "relpos_k": 32, }, "recycling_embedder": { "c_z": c_z, "c_m": c_m, "min_bin": 3.25, "max_bin": 20.75, "no_bins": 15, "inf": inf,#1e8, }, "template": { "distogram": { "min_bin": 3.25, "max_bin": 50.75, "no_bins": 39, }, "template_angle_embedder": { # DISCREPANCY: c_in is supposed to be 51. "c_in": 57, "c_out": c_m, }, "template_pair_embedder": { "c_in": 88, "c_out": c_t, }, "template_pair_stack": { "c_t": c_t, # DISCREPANCY: c_hidden_tri_att here is given in the supplement # as 64. In the code, it's 16. "c_hidden_tri_att": 16, "c_hidden_tri_mul": 64, "no_blocks": 2, "no_heads": 4, "pair_transition_n": 2, "dropout_rate": 0.25, "blocks_per_ckpt": blocks_per_ckpt, "chunk_size": chunk_size, "inf": inf, }, "template_pointwise_attention": { "c_t": c_t, "c_z": c_z, # DISCREPANCY: c_hidden here is given in the supplement as 64. # It's actually 16. "c_hidden": 16, "no_heads": 4, "chunk_size": chunk_size, "inf": inf,#1e-9, }, "inf": inf, "eps": eps,#1e-6, "enabled": True, "embed_angles": True, }, "extra_msa": { "extra_msa_embedder": { "c_in": 25, "c_out": c_e, }, "extra_msa_stack": { "c_m": c_e, "c_z": c_z, "c_hidden_msa_att": 8, "c_hidden_opm": 32, "c_hidden_mul": 128, "c_hidden_pair_att": 32, "no_heads_msa": 8, "no_heads_pair": 4, "no_blocks": 4, "transition_n": 4, "msa_dropout": 0.15, "pair_dropout": 0.25, "blocks_per_ckpt": blocks_per_ckpt, "chunk_size": chunk_size, "inf": inf,#1e9, "eps": eps,#1e-10, }, "enabled": False,#True, }, "evoformer_stack": { "c_m": c_m, "c_z": c_z, "c_hidden_msa_att": 32, "c_hidden_opm": 32, "c_hidden_mul": 128, "c_hidden_pair_att": 32, "c_s": c_s, "no_heads_msa": 8, "no_heads_pair": 4, "no_blocks": 48, "transition_n": 4, "msa_dropout": 0.15, "pair_dropout": 0.25, "blocks_per_ckpt": blocks_per_ckpt, "chunk_size": chunk_size, "inf": inf,#1e9, "eps": eps,#1e-10, }, "structure_module": { "c_s": c_s, "c_z": c_z, "c_ipa": 16, "c_resnet": 128, "no_heads_ipa": 12, "no_qk_points": 4, "no_v_points": 8, "dropout_rate": 0.1, "no_blocks": 8, "no_transition_layers": 1, "no_resnet_blocks": 2, "no_angles": 7, "trans_scale_factor": 10, "epsilon": eps,#1e-12, "inf": inf,#1e5, }, "heads": { "lddt": { "no_bins": 50, "c_in": c_s, "c_hidden": 128, }, "distogram": { "c_z": c_z, "no_bins": aux_distogram_bins, }, "tm_score": { "c_z": c_z, "no_bins": aux_distogram_bins, "enabled": False, }, "masked_msa": { "c_m": c_m, "c_out": 23, }, "experimentally_resolved": { "c_s": c_s, "c_out": 37, }, }, }, "relax": { "max_iterations": 0, # no max "tolerance": 2.39, "stiffness": 10.0, "max_outer_iterations": 20, "exclude_residues": [], }, "loss": { "distogram": { "min_bin": 2.3125, "max_bin": 21.6875, "no_bins": 64, "eps": eps,#1e-6, "weight": 0.,#0.3, }, "experimentally_resolved": { "eps": eps,#1e-8, "min_resolution": 0.1, "max_resolution": 3.0, "weight": 0., }, "fape": { "backbone": { "clamp_distance": 10., "loss_unit_distance": 10., "weight": 0.5, }, "sidechain": { "clamp_distance": 10., "length_scale": 10., "weight": 0.5, }, "eps": 1e-4, "weight": 1.0, }, "lddt": { "min_resolution": 0.1, "max_resolution": 3.0, "cutoff": 15., "no_bins": 50, "eps": eps,#1e-10, "weight": 0.,#0.01, }, "masked_msa": { "eps": eps,#1e-8, "weight": 0.,#2.0, }, "supervised_chi": { "chi_weight": 0.5, "angle_norm_weight": 0.01, "eps": eps,#1e-6, "weight": 0.,#1.0, }, "violation": { "violation_tolerance_factor": 12.0, "clash_overlap_tolerance": 1.5, "eps": eps,#1e-6, "weight": 0., }, "eps": eps, }, })