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- atlas_affinity_cache_min/1aol_A/q.npy +3 -0
- atlas_affinity_cache_min/1aol_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1aol_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1b25_D/meta.json +41 -0
- atlas_affinity_cache_min/1b2s_E/q.npy +3 -0
- atlas_affinity_cache_min/1b2s_E/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1b2s_E/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1b2s_F/meta.json +41 -0
- atlas_affinity_cache_min/1bgf_A/q.npy +3 -0
- atlas_affinity_cache_min/1bgf_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1bgf_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1bxy_A/q.npy +3 -0
- atlas_affinity_cache_min/1bxy_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1bxy_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1by2_A/meta.json +41 -0
- atlas_affinity_cache_min/1dci_C/q.npy +3 -0
- atlas_affinity_cache_min/1dci_C/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dci_C/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dfu_P/q.npy +3 -0
- atlas_affinity_cache_min/1dfu_P/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dfu_P/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dlj_A/q.npy +3 -0
- atlas_affinity_cache_min/1dlj_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dlj_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dpt_A/q.npy +3 -0
- atlas_affinity_cache_min/1dpt_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dpt_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dtd_B/q.npy +3 -0
- atlas_affinity_cache_min/1dtd_B/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1dtd_B/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1egw_B/meta.json +41 -0
- atlas_affinity_cache_min/1ez3_B/q.npy +3 -0
- atlas_affinity_cache_min/1ez3_B/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1ez3_B/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1fd3_A/meta.json +41 -0
- atlas_affinity_cache_min/1fm4_A/q.npy +3 -0
- atlas_affinity_cache_min/1fm4_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1fm4_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1g2r_A/q.npy +3 -0
- atlas_affinity_cache_min/1g2r_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1g2r_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1gnt_A/q.npy +3 -0
- atlas_affinity_cache_min/1gnt_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1gnt_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1gwe_A/meta.json +41 -0
- atlas_affinity_cache_min/1h16_A/q.npy +3 -0
- atlas_affinity_cache_min/1h16_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1h16_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1hc9_B/meta.json +41 -0
- atlas_affinity_cache_min/1hp1_A/q.npy +3 -0
atlas_affinity_cache_min/1aol_A/q.npy
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atlas_affinity_cache_min/1aol_A/topk_neighbors.npy
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atlas_affinity_cache_min/1aol_A/topk_weights.npy
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atlas_affinity_cache_min/1b25_D/meta.json
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{
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"entry": "1b25_D",
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"n_frames": 3003,
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"n_ca": 619,
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"n_replicates": 3,
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"rep_names": [
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"R1",
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"R2",
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"R3"
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],
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"traj_lengths": [
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1001,
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1001,
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1001
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],
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"xtc_files": [
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"1b25_D_R1.xtc",
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"1b25_D_R2.xtc",
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"1b25_D_R3.xtc"
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],
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| 21 |
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"pca_dim": 50,
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| 22 |
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"tica_dim": 3,
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| 23 |
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"tica_evals": [
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0.9894677996635437,
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"lag": 10,
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"sigma_k": 30,
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"top_k": 64,
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"contact_cutoff_A": 12.0,
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| 32 |
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"min_seq_sep": 3,
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| 33 |
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"max_pairs": 20000,
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| 34 |
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"n_ca_pairs_used": 9802,
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| 35 |
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"feature": "CA_pairwise_distances",
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| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
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| 38 |
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"dtype_q": "float32",
|
| 39 |
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"dtype_topk_neighbors": "uint16",
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| 40 |
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"dtype_topk_weights": "float16"
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}
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atlas_affinity_cache_min/1b2s_E/q.npy
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atlas_affinity_cache_min/1b2s_E/topk_neighbors.npy
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atlas_affinity_cache_min/1b2s_E/topk_weights.npy
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atlas_affinity_cache_min/1b2s_F/meta.json
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{
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"entry": "1b2s_F",
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| 3 |
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"n_frames": 3003,
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| 4 |
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"n_ca": 90,
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"n_replicates": 3,
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| 6 |
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"rep_names": [
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| 7 |
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"R1",
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| 8 |
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"R2",
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| 9 |
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"R3"
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| 10 |
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],
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| 11 |
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"traj_lengths": [
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| 12 |
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1001,
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1001,
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| 14 |
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1001
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],
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| 16 |
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"xtc_files": [
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| 17 |
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"1b2s_F_R1.xtc",
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| 18 |
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"1b2s_F_R2.xtc",
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| 19 |
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"1b2s_F_R3.xtc"
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| 20 |
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],
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| 21 |
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"pca_dim": 50,
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| 22 |
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"tica_dim": 3,
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| 23 |
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"tica_evals": [
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0.9300863146781921,
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0.870855450630188,
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"lag": 10,
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| 29 |
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"sigma_k": 30,
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| 30 |
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"top_k": 64,
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| 31 |
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"contact_cutoff_A": 12.0,
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| 32 |
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"min_seq_sep": 3,
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| 33 |
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"max_pairs": 20000,
|
| 34 |
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"n_ca_pairs_used": 906,
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| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
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"dtype_q": "float32",
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| 39 |
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"dtype_topk_neighbors": "uint16",
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| 40 |
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"dtype_topk_weights": "float16"
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}
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atlas_affinity_cache_min/1bgf_A/q.npy
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atlas_affinity_cache_min/1bgf_A/topk_neighbors.npy
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version https://git-lfs.github.com/spec/v1
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atlas_affinity_cache_min/1bgf_A/topk_weights.npy
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atlas_affinity_cache_min/1bxy_A/q.npy
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atlas_affinity_cache_min/1bxy_A/topk_neighbors.npy
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version https://git-lfs.github.com/spec/v1
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atlas_affinity_cache_min/1bxy_A/topk_weights.npy
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atlas_affinity_cache_min/1by2_A/meta.json
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{
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"entry": "1by2_A",
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"R3"
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],
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1001,
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1001,
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1001
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"xtc_files": [
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| 17 |
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"1by2_A_R2.xtc",
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"1by2_A_R3.xtc"
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| 20 |
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],
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"pca_dim": 50,
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"tica_dim": 3,
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"tica_evals": [
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"lag": 10,
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"sigma_k": 30,
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"top_k": 64,
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| 31 |
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"contact_cutoff_A": 12.0,
|
| 32 |
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"min_seq_sep": 3,
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| 33 |
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"max_pairs": 20000,
|
| 34 |
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"n_ca_pairs_used": 1548,
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| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
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"dtype_q": "float32",
|
| 39 |
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"dtype_topk_neighbors": "uint16",
|
| 40 |
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"dtype_topk_weights": "float16"
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| 41 |
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}
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atlas_affinity_cache_min/1dci_C/q.npy
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version https://git-lfs.github.com/spec/v1
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atlas_affinity_cache_min/1dci_C/topk_neighbors.npy
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version https://git-lfs.github.com/spec/v1
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atlas_affinity_cache_min/1dci_C/topk_weights.npy
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version https://git-lfs.github.com/spec/v1
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atlas_affinity_cache_min/1dfu_P/q.npy
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version https://git-lfs.github.com/spec/v1
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ADDED
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ADDED
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ADDED
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ADDED
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atlas_affinity_cache_min/1dtd_B/q.npy
ADDED
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ADDED
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ADDED
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atlas_affinity_cache_min/1egw_B/meta.json
ADDED
|
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| 1 |
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1001,
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|
| 17 |
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| 18 |
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| 19 |
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|
| 20 |
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],
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|
| 22 |
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| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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|
| 34 |
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|
| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
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"dtype_q": "float32",
|
| 39 |
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"dtype_topk_neighbors": "uint16",
|
| 40 |
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"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1ez3_B/q.npy
ADDED
|
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atlas_affinity_cache_min/1ez3_B/topk_neighbors.npy
ADDED
|
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ADDED
|
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atlas_affinity_cache_min/1fd3_A/meta.json
ADDED
|
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|
| 32 |
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|
| 33 |
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|
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|
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"feature": "CA_pairwise_distances",
|
| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
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| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
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|
| 39 |
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"dtype_topk_neighbors": "uint16",
|
| 40 |
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"dtype_topk_weights": "float16"
|
| 41 |
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}
|
atlas_affinity_cache_min/1fm4_A/q.npy
ADDED
|
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ADDED
|
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ADDED
|
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atlas_affinity_cache_min/1g2r_A/q.npy
ADDED
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ADDED
|
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ADDED
|
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ADDED
|
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ADDED
|
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ADDED
|
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atlas_affinity_cache_min/1gwe_A/meta.json
ADDED
|
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|
| 1 |
+
{
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| 2 |
+
"entry": "1gwe_A",
|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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"R1",
|
| 8 |
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"R2",
|
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|
| 10 |
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],
|
| 11 |
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|
| 12 |
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1001,
|
| 13 |
+
1001,
|
| 14 |
+
1001
|
| 15 |
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],
|
| 16 |
+
"xtc_files": [
|
| 17 |
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"1gwe_A_R1.xtc",
|
| 18 |
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"1gwe_A_R2.xtc",
|
| 19 |
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"1gwe_A_R3.xtc"
|
| 20 |
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],
|
| 21 |
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|
| 22 |
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|
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|
| 25 |
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|
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| 28 |
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|
| 29 |
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|
| 30 |
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"top_k": 64,
|
| 31 |
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"contact_cutoff_A": 12.0,
|
| 32 |
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"min_seq_sep": 3,
|
| 33 |
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"max_pairs": 20000,
|
| 34 |
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"n_ca_pairs_used": 5908,
|
| 35 |
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"feature": "CA_pairwise_distances",
|
| 36 |
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"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
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"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
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"dtype_q": "float32",
|
| 39 |
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"dtype_topk_neighbors": "uint16",
|
| 40 |
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"dtype_topk_weights": "float16"
|
| 41 |
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}
|
atlas_affinity_cache_min/1h16_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
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|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:9d9251ebf0e7ba8ea5bcf0d0299aa9a48fb5567a744a048021c840bb99a66b9e
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1h16_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:549264b023cf67a1ed9d6d41875a0fbf8108ccfbef43770aacbd4a93be6c6a62
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1h16_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:9fb123e6f1c345c82d6f8e5de053a4ebaf024d1e80d854de6752da3071dda121
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1hc9_B/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1hc9_B",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 74,
|
| 5 |
+
"n_replicates": 3,
|
| 6 |
+
"rep_names": [
|
| 7 |
+
"R1",
|
| 8 |
+
"R2",
|
| 9 |
+
"R3"
|
| 10 |
+
],
|
| 11 |
+
"traj_lengths": [
|
| 12 |
+
1001,
|
| 13 |
+
1001,
|
| 14 |
+
1001
|
| 15 |
+
],
|
| 16 |
+
"xtc_files": [
|
| 17 |
+
"1hc9_B_R1.xtc",
|
| 18 |
+
"1hc9_B_R2.xtc",
|
| 19 |
+
"1hc9_B_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9534931182861328,
|
| 25 |
+
0.9070484042167664,
|
| 26 |
+
0.830098569393158
|
| 27 |
+
],
|
| 28 |
+
"lag": 10,
|
| 29 |
+
"sigma_k": 30,
|
| 30 |
+
"top_k": 64,
|
| 31 |
+
"contact_cutoff_A": 12.0,
|
| 32 |
+
"min_seq_sep": 3,
|
| 33 |
+
"max_pairs": 20000,
|
| 34 |
+
"n_ca_pairs_used": 697,
|
| 35 |
+
"feature": "CA_pairwise_distances",
|
| 36 |
+
"affinity": "exp(-||q_i-q_j||^2/(sigma_i*sigma_j))",
|
| 37 |
+
"note": "Minimal training cache. Only q, top-k neighbors, top-k weights, and meta are saved.",
|
| 38 |
+
"dtype_q": "float32",
|
| 39 |
+
"dtype_topk_neighbors": "uint16",
|
| 40 |
+
"dtype_topk_weights": "float16"
|
| 41 |
+
}
|
atlas_affinity_cache_min/1hp1_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:52bb5ef089c62e302d5acc6196f16be00f69d539d67829360565a1606f43c581
|
| 3 |
+
size 36164
|