ZhiyuanChen's picture
Publish OFoldX pipeline artifacts
c2261e7 verified
Raw
History Blame Contribute Delete
3.64 kB
{
"source": "RosettaCommons/RFdiffusion",
"checkpoint_variant": "Complex_base_ckpt",
"model": {
"num_extra_blocks": 4,
"num_main_blocks": 32,
"num_refinement_blocks": 4,
"msa_size": 256,
"full_msa_size": 64,
"pair_size": 128,
"template_size": 64,
"num_msa_attention_heads": 8,
"num_pair_attention_heads": 4,
"num_template_attention_heads": 4,
"hidden_size": 32,
"template_hidden_size": 32,
"dropout": 0.15,
"time_embedding_size": 0,
"time_embedding_projection_size": 10,
"freeze_track_motif": false,
"use_motif_timestep": true,
"se3_param_full": {
"num_layers": 1,
"num_channels": 32,
"num_degrees": 2,
"num_attention_heads": 4,
"div": 4,
"l0_in_features": 8,
"l0_out_features": 8,
"l1_in_features": 3,
"l1_out_features": 2,
"num_edge_features": 32
},
"se3_param_topk": {
"num_layers": 1,
"num_channels": 32,
"num_degrees": 2,
"num_attention_heads": 4,
"div": 4,
"l0_in_features": 64,
"l0_out_features": 64,
"l1_in_features": 3,
"l1_out_features": 2,
"num_edge_features": 64
},
"vocab_size": 21
},
"diffuser": {
"num_timesteps": 50,
"b_0": 0.01,
"b_T": 0.07,
"min_b": 1.5,
"max_b": 2.5,
"min_sigma": 0.02,
"max_sigma": 1.5,
"schedule_type": "linear",
"so3_schedule_type": "linear",
"so3_type": "igso3",
"crd_scale": 0.25,
"partial_timesteps": null,
"truncation_level": 2000,
"igso3_num_omega": 1000,
"igso3_num_sigma": 500
},
"preprocess": {
"sidechain_input": false,
"motif_sidechain_input": true,
"template_1d_size": 24,
"template_2d_size": 44,
"predict_previous": false,
"prob_self_cond": 0.5,
"str_self_cond": true
},
"denoiser": {
"noise_scale_ca": 1.0,
"final_noise_scale_ca": 1.0,
"ca_noise_schedule_type": "constant",
"noise_scale_frame": 1.0,
"final_noise_scale_frame": 1.0,
"frame_noise_schedule_type": "constant"
},
"inference": {
"input_pdb": null,
"num_designs": 1,
"design_startnum": 0,
"ckpt_override_path": null,
"symmetry": null,
"recenter": true,
"radius": 10.0,
"model_only_neighbors": false,
"output_prefix": "samples/design",
"write_trajectory": false,
"empty_cache_per_design": false,
"scaffold_guided": false,
"model_runner": "SelfConditioning",
"cautious": true,
"align_motif": true,
"symmetric_self_cond": true,
"final_step": 1,
"deterministic": false,
"trb_save_ckpt_path": null,
"schedule_directory_path": null,
"model_directory_path": null,
"cyclic": false,
"cyc_chains": "a"
},
"contigmap": {
"contigs": null,
"inpaint_seq": null,
"inpaint_str": null,
"inpaint_str_helix": null,
"inpaint_str_strand": null,
"inpaint_str_loop": null,
"provide_seq": null,
"length": null
},
"ppi": {
"hotspot_res": null
},
"potentials": {
"guiding_potentials": null,
"guide_scale": 10.0,
"guide_decay": "constant",
"olig_inter_all": null,
"olig_intra_all": null,
"olig_custom_contact": null,
"substrate": null
},
"scaffoldguided": {
"scaffoldguided": false,
"target_pdb": false,
"target_path": null,
"scaffold_list": null,
"scaffold_dir": null,
"sampled_insertion": 0,
"sampled_N": 0,
"sampled_C": 0,
"ss_mask": 0,
"systematic": false,
"target_ss": null,
"target_adj": null,
"mask_loops": true,
"contig_crop": null
},
"logging": {
"inputs": false
}
}