Add files using upload-large-folder tool
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- atlas_affinity_cache_min/16pk_A/meta.json +41 -0
- atlas_affinity_cache_min/1ah7_A/meta.json +41 -0
- atlas_affinity_cache_min/1b2s_E/meta.json +41 -0
- atlas_affinity_cache_min/1bkp_A/meta.json +41 -0
- atlas_affinity_cache_min/1btk_A/meta.json +41 -0
- atlas_affinity_cache_min/1bx7_A/q.npy +3 -0
- atlas_affinity_cache_min/1bx7_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1bx7_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1bxy_A/meta.json +41 -0
- atlas_affinity_cache_min/1cuo_A/q.npy +3 -0
- atlas_affinity_cache_min/1cuo_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1cuo_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1d2t_A/q.npy +3 -0
- atlas_affinity_cache_min/1d2t_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1d2t_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1doi_A/q.npy +3 -0
- atlas_affinity_cache_min/1doi_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1doi_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1dpt_A/meta.json +41 -0
- atlas_affinity_cache_min/1ear_A/q.npy +3 -0
- atlas_affinity_cache_min/1ear_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1ear_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1ef1_D/meta.json +41 -0
- atlas_affinity_cache_min/1ez3_B/meta.json +41 -0
- atlas_affinity_cache_min/1f20_A/q.npy +3 -0
- atlas_affinity_cache_min/1f20_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1f20_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1f3u_G/q.npy +3 -0
- atlas_affinity_cache_min/1f3u_G/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1f3u_G/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1f9p_A/meta.json +41 -0
- atlas_affinity_cache_min/1fm4_A/meta.json +41 -0
- atlas_affinity_cache_min/1fn9_A/q.npy +3 -0
- atlas_affinity_cache_min/1fn9_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1fn9_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1fs1_A/meta.json +41 -0
- atlas_affinity_cache_min/1fx4_A/meta.json +41 -0
- atlas_affinity_cache_min/1fxo_G/meta.json +41 -0
- atlas_affinity_cache_min/1g38_A/q.npy +3 -0
- atlas_affinity_cache_min/1g38_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1g38_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1g6g_A/q.npy +3 -0
- atlas_affinity_cache_min/1g6g_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1g6g_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1g7s_A/q.npy +3 -0
- atlas_affinity_cache_min/1g7s_A/topk_neighbors.npy +3 -0
- atlas_affinity_cache_min/1g7s_A/topk_weights.npy +3 -0
- atlas_affinity_cache_min/1gqe_A/meta.json +41 -0
- atlas_affinity_cache_min/1gqv_A/q.npy +3 -0
- atlas_affinity_cache_min/1gqv_A/topk_neighbors.npy +3 -0
atlas_affinity_cache_min/16pk_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "16pk_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 415,
|
| 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 |
+
"16pk_A_R1.xtc",
|
| 18 |
+
"16pk_A_R2.xtc",
|
| 19 |
+
"16pk_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9645382165908813,
|
| 25 |
+
0.9460870623588562,
|
| 26 |
+
0.9314114451408386
|
| 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": 5802,
|
| 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/1ah7_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1ah7_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 245,
|
| 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 |
+
"1ah7_A_R1.xtc",
|
| 18 |
+
"1ah7_A_R2.xtc",
|
| 19 |
+
"1ah7_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9811980128288269,
|
| 25 |
+
0.9739657044410706,
|
| 26 |
+
0.9220118522644043
|
| 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": 3278,
|
| 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/1b2s_E/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1b2s_E",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 90,
|
| 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 |
+
"1b2s_E_R1.xtc",
|
| 18 |
+
"1b2s_E_R2.xtc",
|
| 19 |
+
"1b2s_E_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9063084125518799,
|
| 25 |
+
0.8316266536712646,
|
| 26 |
+
0.6883992552757263
|
| 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": 926,
|
| 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/1bkp_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1bkp_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 278,
|
| 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 |
+
"1bkp_A_R1.xtc",
|
| 18 |
+
"1bkp_A_R2.xtc",
|
| 19 |
+
"1bkp_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9835923910140991,
|
| 25 |
+
0.9721259474754333,
|
| 26 |
+
0.9376500844955444
|
| 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": 3175,
|
| 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/1btk_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1btk_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 169,
|
| 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 |
+
"1btk_A_R1.xtc",
|
| 18 |
+
"1btk_A_R2.xtc",
|
| 19 |
+
"1btk_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9361371397972107,
|
| 25 |
+
0.9218696355819702,
|
| 26 |
+
0.9012670516967773
|
| 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": 1749,
|
| 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/1bx7_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:351d1be46288159d081b9a32b23d92783c48f2e6f56c354031b48a19af2d1f76
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1bx7_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:855dc77df8aceddf85e3186b6265951b94463f27c114e34a75f0c20195d15a5a
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1bx7_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ea7f1972f1ecf78b09817c69b36d7835b979ac98b5f2be126c34f9b5bd87b459
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1bxy_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1bxy_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 60,
|
| 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 |
+
"1bxy_A_R1.xtc",
|
| 18 |
+
"1bxy_A_R2.xtc",
|
| 19 |
+
"1bxy_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.8442957401275635,
|
| 25 |
+
0.7777894139289856,
|
| 26 |
+
0.6193963289260864
|
| 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": 561,
|
| 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/1cuo_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:3f2416a3d961bd955fa1ca2227b32a95faece1b4b694e7ec3567536e0965b533
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1cuo_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:d8a4390ea200df6f366cdfe5e8fb03cf78b27a9577c0247879a4e4f5840dd50d
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1cuo_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2b04f7a9901e6f53b3f626659ca107154b18ada4f2eac38586afff85bdad6b2c
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1d2t_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a892f77521e0a176a2a8d0299b2fa220b3c0498addc40eb867e780d8794fb946
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1d2t_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:86cc2b1b8bc409f5b74f833e4532adc17cc59b326b0e17287d4d57b9ee457f44
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1d2t_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:48fbd27251a48bf291b064bc6377d6f1df434b825ef92ea25217c0a47dd595d8
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1doi_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:48f84ca2c6f738ec890dd67b93a72b4a280c5ae3b6118309f678a3d7f4520819
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1doi_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:f93b670921d64c091ca83a93f7e041b775637d9848146ab70cf3809932aea20e
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1doi_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:587006e09d31e6112766c7fc81d891f8392aed83be99946231534385517f9d10
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1dpt_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1dpt_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 117,
|
| 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 |
+
"1dpt_A_R1.xtc",
|
| 18 |
+
"1dpt_A_R2.xtc",
|
| 19 |
+
"1dpt_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.932632327079773,
|
| 25 |
+
0.9220508337020874,
|
| 26 |
+
0.8990135788917542
|
| 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": 1148,
|
| 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/1ear_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e063c5bd37ce26921677b25367e9f2d62031c39fd8ad163b148cdde40650448e
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1ear_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e5a8e0dbd6b3316f939a9244f1a0eda46711d0fa84584984c73be2598a0eab72
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1ear_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:7aca7a45cecf093d6f25c79573aa41e4c167ce89a56495b77be35aeac64b9201
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1ef1_D/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1ef1_D",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 90,
|
| 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 |
+
"1ef1_D_R1.xtc",
|
| 18 |
+
"1ef1_D_R2.xtc",
|
| 19 |
+
"1ef1_D_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.989753246307373,
|
| 25 |
+
0.9861642122268677,
|
| 26 |
+
0.9778985381126404
|
| 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": 413,
|
| 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/1ez3_B/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1ez3_B",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 127,
|
| 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 |
+
"1ez3_B_R1.xtc",
|
| 18 |
+
"1ez3_B_R2.xtc",
|
| 19 |
+
"1ez3_B_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9287376403808594,
|
| 25 |
+
0.8289002180099487,
|
| 26 |
+
0.7730521559715271
|
| 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": 1133,
|
| 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/1f20_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:fcdc232309d5cdca03a08596ecad012339c181291d6c160c0b34f21627479640
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1f20_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:aa8d1d1387e7dcb845c54a82a1a254eaa1a0c7f22fbdc6ebf310af5672d1853a
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1f20_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:d7fcb555ee899c0919184546d4999b5c33a7cd0620486619f34f2fe8b0b28ba6
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1f3u_G/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:43a9e13b821740cc7fdccb49431aeccfbc4e86745002662fb3fc49bec1a3431b
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1f3u_G/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:29a7ec00c8188d909e9eaf75b0480d2c41050ecdf5659953698d6fd74ec04a71
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1f3u_G/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b48cc1212cb566378fd60ad410064bf71796574f4c7e8945b5eb5ce434e52840
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1f9p_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1f9p_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 85,
|
| 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 |
+
"1f9p_A_R1.xtc",
|
| 18 |
+
"1f9p_A_R2.xtc",
|
| 19 |
+
"1f9p_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9758711457252502,
|
| 25 |
+
0.9622182846069336,
|
| 26 |
+
0.9379040002822876
|
| 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": 650,
|
| 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/1fm4_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1fm4_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 159,
|
| 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 |
+
"1fm4_A_R1.xtc",
|
| 18 |
+
"1fm4_A_R2.xtc",
|
| 19 |
+
"1fm4_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9327874779701233,
|
| 25 |
+
0.8756321668624878,
|
| 26 |
+
0.8217353820800781
|
| 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": 1682,
|
| 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/1fn9_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:8d2597116a3c45d82850a5de8136c49791207ba1bdc8dc0099f22f7a82936875
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1fn9_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:853d1a39a8006bc647753c51a8fd0237b94e774d59b61fd54b51248ec441aa7d
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1fn9_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c55733fd592013abe816e3c88552068a6479c2ce19090ee83ee4c954f1308c42
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1fs1_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1fs1_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 53,
|
| 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 |
+
"1fs1_A_R1.xtc",
|
| 18 |
+
"1fs1_A_R2.xtc",
|
| 19 |
+
"1fs1_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9643642902374268,
|
| 25 |
+
0.9599249958992004,
|
| 26 |
+
0.9033858776092529
|
| 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": 352,
|
| 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/1fx4_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1fx4_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 231,
|
| 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 |
+
"1fx4_A_R1.xtc",
|
| 18 |
+
"1fx4_A_R2.xtc",
|
| 19 |
+
"1fx4_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9679055213928223,
|
| 25 |
+
0.9575130343437195,
|
| 26 |
+
0.9040732979774475
|
| 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": 2795,
|
| 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/1fxo_G/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1fxo_G",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 293,
|
| 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 |
+
"1fxo_G_R1.xtc",
|
| 18 |
+
"1fxo_G_R2.xtc",
|
| 19 |
+
"1fxo_G_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9892376065254211,
|
| 25 |
+
0.9830611944198608,
|
| 26 |
+
0.9593947529792786
|
| 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": 3665,
|
| 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/1g38_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:147a228b6d6a21c784f1db8d32ac159f10f6aa26b0f8b031e390fdf8f745a305
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1g38_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:9956f3486f2edc3b050fc7680033f74661990150bfc30984ef8d2f27448d0165
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1g38_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2462b8e68deb346b2d284d19aeb42def0ecfb6bcfb7e9b9658bf85b387d2c200
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1g6g_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:0926cf4e50f326b2125285b487e8aa446f2e591a514b92d51b680de6287a89eb
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1g6g_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:881550cacd9cffb17c9b4fd4ee3122393ccaad35d31d7712dd9fa9abcd0707f0
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1g6g_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:def94bcbb1112ad7c1bd8015b7c2bb0a03fec39b1f8999948309e687a8a6921a
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1g7s_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:eb3647264c1ed8cc2560acf5e9df12bb1252f4842de67c1bfbd3946caebb79a4
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1g7s_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:40320fc6b797bfc23458e97dd25b3dbca92dc67355fb5091191e9fc05d7036ec
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1g7s_A/topk_weights.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:2fb446d248f2691c4d1a983e17d9f7cde2a26ff9066ce0ec1b27de7e55b7759c
|
| 3 |
+
size 384512
|
atlas_affinity_cache_min/1gqe_A/meta.json
ADDED
|
@@ -0,0 +1,41 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"entry": "1gqe_A",
|
| 3 |
+
"n_frames": 3003,
|
| 4 |
+
"n_ca": 365,
|
| 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 |
+
"1gqe_A_R1.xtc",
|
| 18 |
+
"1gqe_A_R2.xtc",
|
| 19 |
+
"1gqe_A_R3.xtc"
|
| 20 |
+
],
|
| 21 |
+
"pca_dim": 50,
|
| 22 |
+
"tica_dim": 3,
|
| 23 |
+
"tica_evals": [
|
| 24 |
+
0.9923786520957947,
|
| 25 |
+
0.9879216551780701,
|
| 26 |
+
0.9713122844696045
|
| 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": 4070,
|
| 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/1gqv_A/q.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:eda304bf88709a5a713b0bbb9e2cf241f7ba1dd600310c6a6c154183333a81da
|
| 3 |
+
size 36164
|
atlas_affinity_cache_min/1gqv_A/topk_neighbors.npy
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:57fe68ea7c5715cd292bf4be7a8b392ba9fd7c83c9be5cb0e2332fee97fe1815
|
| 3 |
+
size 384512
|