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inference: |
|
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input_pdb: null |
|
|
num_designs: 10 |
|
|
design_startnum: 0 |
|
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ckpt_override_path: null |
|
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symmetry: null |
|
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recenter: True |
|
|
radius: 10.0 |
|
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model_only_neighbors: False |
|
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output_prefix: samples/design |
|
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write_trajectory: True |
|
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scaffold_guided: False |
|
|
model_runner: SelfConditioning |
|
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cautious: True |
|
|
align_motif: True |
|
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symmetric_self_cond: True |
|
|
final_step: 1 |
|
|
deterministic: False |
|
|
trb_save_ckpt_path: null |
|
|
schedule_directory_path: null |
|
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model_directory_path: null |
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|
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contigmap: |
|
|
contigs: null |
|
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inpaint_seq: null |
|
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provide_seq: null |
|
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length: null |
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model: |
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n_extra_block: 4 |
|
|
n_main_block: 32 |
|
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n_ref_block: 4 |
|
|
d_msa: 256 |
|
|
d_msa_full: 64 |
|
|
d_pair: 128 |
|
|
d_templ: 64 |
|
|
n_head_msa: 8 |
|
|
n_head_pair: 4 |
|
|
n_head_templ: 4 |
|
|
d_hidden: 32 |
|
|
d_hidden_templ: 32 |
|
|
p_drop: 0.15 |
|
|
SE3_param_full: |
|
|
num_layers: 1 |
|
|
num_channels: 32 |
|
|
num_degrees: 2 |
|
|
n_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 |
|
|
n_heads: 4 |
|
|
div: 4 |
|
|
l0_in_features: 64 |
|
|
l0_out_features: 64 |
|
|
l1_in_features: 3 |
|
|
l1_out_features: 2 |
|
|
num_edge_features: 64 |
|
|
freeze_track_motif: False |
|
|
use_motif_timestep: False |
|
|
|
|
|
diffuser: |
|
|
T: 50 |
|
|
b_0: 1e-2 |
|
|
b_T: 7e-2 |
|
|
schedule_type: linear |
|
|
so3_type: igso3 |
|
|
crd_scale: 0.25 |
|
|
partial_T: null |
|
|
so3_schedule_type: linear |
|
|
min_b: 1.5 |
|
|
max_b: 2.5 |
|
|
min_sigma: 0.02 |
|
|
max_sigma: 1.5 |
|
|
|
|
|
denoiser: |
|
|
noise_scale_ca: 1 |
|
|
final_noise_scale_ca: 1 |
|
|
ca_noise_schedule_type: constant |
|
|
noise_scale_frame: 1 |
|
|
final_noise_scale_frame: 1 |
|
|
frame_noise_schedule_type: constant |
|
|
|
|
|
ppi: |
|
|
hotspot_res: null |
|
|
|
|
|
potentials: |
|
|
guiding_potentials: null |
|
|
guide_scale: 10 |
|
|
guide_decay: constant |
|
|
olig_inter_all : null |
|
|
olig_intra_all : null |
|
|
olig_custom_contact : null |
|
|
substrate: null |
|
|
|
|
|
contig_settings: |
|
|
ref_idx: null |
|
|
hal_idx: null |
|
|
idx_rf: null |
|
|
inpaint_seq_tensor: null |
|
|
|
|
|
preprocess: |
|
|
sidechain_input: False |
|
|
motif_sidechain_input: True |
|
|
d_t1d: 22 |
|
|
d_t2d: 44 |
|
|
prob_self_cond: 0.0 |
|
|
str_self_cond: False |
|
|
predict_previous: False |
|
|
|
|
|
logging: |
|
|
inputs: False |
|
|
|
|
|
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 |
|
|
|
