Commit
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98ff12f
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Parent(s):
489e702
Upload 8 files
Browse files- model_1_ptm/config.json +945 -0
- model_1_ptm/pytorch_model.bin +3 -0
- model_2_ptm/config.json +945 -0
- model_2_ptm/pytorch_model.bin +3 -0
- model_4_ptm/config.json +945 -0
- model_4_ptm/pytorch_model.bin +3 -0
- model_5_ptm/config.json +945 -0
- model_5_ptm/pytorch_model.bin +3 -0
model_1_ptm/config.json
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|
| 1 |
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| 2 |
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| 3 |
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| 934 |
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| 937 |
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| 939 |
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| 940 |
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| 941 |
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| 942 |
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| 944 |
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|
| 945 |
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|
model_1_ptm/pytorch_model.bin
ADDED
|
@@ -0,0 +1,3 @@
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|
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+
version https://git-lfs.github.com/spec/v1
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oid sha256:ca0c630b0601bdcf6a6bc206293d4c685d33a1cb9f8cd94df9ac06b4cce34e52
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| 3 |
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size 374784719
|
model_2_ptm/config.json
ADDED
|
@@ -0,0 +1,945 @@
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|
| 1 |
+
{
|
| 2 |
+
"CONFIG": {
|
| 3 |
+
"data": {
|
| 4 |
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"transform": {
|
| 5 |
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"common": {
|
| 6 |
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"crop_size": {
|
| 7 |
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"eval": null,
|
| 8 |
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"finetune": 384,
|
| 9 |
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"predict": null,
|
| 10 |
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"train": 256
|
| 11 |
+
},
|
| 12 |
+
"feats": {
|
| 13 |
+
"aatype": [
|
| 14 |
+
"num residues placeholder"
|
| 15 |
+
],
|
| 16 |
+
"all_atom_mask": [
|
| 17 |
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"num residues placeholder",
|
| 18 |
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null
|
| 19 |
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],
|
| 20 |
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"all_atom_positions": [
|
| 21 |
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|
| 22 |
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null,
|
| 23 |
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null
|
| 24 |
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|
| 25 |
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|
| 26 |
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"num residues placeholder",
|
| 27 |
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null
|
| 28 |
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],
|
| 29 |
+
"assembly_num_chains": [
|
| 30 |
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null
|
| 31 |
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],
|
| 32 |
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|
| 33 |
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"num residues placeholder"
|
| 34 |
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],
|
| 35 |
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"asym_len": [
|
| 36 |
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null
|
| 37 |
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],
|
| 38 |
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"atom14_alt_gt_exists": [
|
| 39 |
+
"num residues placeholder",
|
| 40 |
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null
|
| 41 |
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],
|
| 42 |
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"atom14_alt_gt_positions": [
|
| 43 |
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"num residues placeholder",
|
| 44 |
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null,
|
| 45 |
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null
|
| 46 |
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],
|
| 47 |
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|
| 48 |
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"num residues placeholder",
|
| 49 |
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null
|
| 50 |
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],
|
| 51 |
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"atom14_atom_is_ambiguous": [
|
| 52 |
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"num residues placeholder",
|
| 53 |
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null
|
| 54 |
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],
|
| 55 |
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|
| 56 |
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|
| 57 |
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null
|
| 58 |
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],
|
| 59 |
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|
| 60 |
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|
| 61 |
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null,
|
| 62 |
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null
|
| 63 |
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],
|
| 64 |
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|
| 65 |
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"num residues placeholder",
|
| 66 |
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null
|
| 67 |
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],
|
| 68 |
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"backbone_rigid_mask": [
|
| 69 |
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"num residues placeholder"
|
| 70 |
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|
| 71 |
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"backbone_rigid_tensor": [
|
| 72 |
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|
| 73 |
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null,
|
| 74 |
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null
|
| 75 |
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|
| 76 |
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"bert_mask": [
|
| 77 |
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|
| 78 |
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"num residues placeholder"
|
| 79 |
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],
|
| 80 |
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"chi_angles_sin_cos": [
|
| 81 |
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"num residues placeholder",
|
| 82 |
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null,
|
| 83 |
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null
|
| 84 |
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],
|
| 85 |
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"chi_mask": [
|
| 86 |
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"num residues placeholder",
|
| 87 |
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null
|
| 88 |
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],
|
| 89 |
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"cluster_bias_mask": [
|
| 90 |
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|
| 91 |
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],
|
| 92 |
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"entity_id": [
|
| 93 |
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"num residues placeholder"
|
| 94 |
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],
|
| 95 |
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"extra_deletion_value": [
|
| 96 |
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|
| 97 |
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"num residues placeholder"
|
| 98 |
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],
|
| 99 |
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"extra_has_deletion": [
|
| 100 |
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|
| 101 |
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"num residues placeholder"
|
| 102 |
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],
|
| 103 |
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"extra_msa": [
|
| 104 |
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"extra msa placeholder",
|
| 105 |
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"num residues placeholder"
|
| 106 |
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],
|
| 107 |
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"extra_msa_mask": [
|
| 108 |
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|
| 109 |
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"num residues placeholder"
|
| 110 |
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],
|
| 111 |
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"extra_msa_row_mask": [
|
| 112 |
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"extra msa placeholder"
|
| 113 |
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],
|
| 114 |
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"is_distillation": [],
|
| 115 |
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"msa_feat": [
|
| 116 |
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|
| 117 |
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"num residues placeholder",
|
| 118 |
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null
|
| 119 |
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],
|
| 120 |
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|
| 121 |
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|
| 122 |
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"num residues placeholder"
|
| 123 |
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],
|
| 124 |
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"msa_row_mask": [
|
| 125 |
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|
| 126 |
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],
|
| 127 |
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"no_recycling_iters": [],
|
| 128 |
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"num_sym": [
|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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null
|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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|
| 143 |
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null
|
| 144 |
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|
| 145 |
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|
| 146 |
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"num residues placeholder",
|
| 147 |
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null
|
| 148 |
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],
|
| 149 |
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"resolution": [],
|
| 150 |
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|
| 151 |
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|
| 152 |
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null,
|
| 153 |
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null,
|
| 154 |
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null
|
| 155 |
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|
| 156 |
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|
| 157 |
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"num residues placeholder",
|
| 158 |
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null
|
| 159 |
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|
| 160 |
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|
| 161 |
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"num residues placeholder",
|
| 162 |
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null
|
| 163 |
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],
|
| 164 |
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|
| 165 |
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"num residues placeholder",
|
| 166 |
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null
|
| 167 |
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],
|
| 168 |
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"rigidgroups_gt_frames": [
|
| 169 |
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"num residues placeholder",
|
| 170 |
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null,
|
| 171 |
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null,
|
| 172 |
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null
|
| 173 |
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],
|
| 174 |
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"seq_length": [],
|
| 175 |
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"seq_mask": [
|
| 176 |
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"num residues placeholder"
|
| 177 |
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],
|
| 178 |
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"sym_id": [
|
| 179 |
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"num residues placeholder"
|
| 180 |
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],
|
| 181 |
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"target_feat": [
|
| 182 |
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"num residues placeholder",
|
| 183 |
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null
|
| 184 |
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|
| 185 |
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|
| 186 |
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|
| 187 |
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"num residues placeholder"
|
| 188 |
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],
|
| 189 |
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|
| 190 |
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|
| 191 |
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"num residues placeholder",
|
| 192 |
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null
|
| 193 |
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|
| 194 |
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"model.structure_module.position_scale": 20,
|
| 929 |
+
"model.structure_module.separate_kv": true,
|
| 930 |
+
"model.template_pair_stack.attention_first": false
|
| 931 |
+
},
|
| 932 |
+
"model_5_ptm": {
|
| 933 |
+
"model.auxiliary_heads.tm_enabled": true
|
| 934 |
+
}
|
| 935 |
+
},
|
| 936 |
+
"_config": null,
|
| 937 |
+
"architectures": [
|
| 938 |
+
"STFold"
|
| 939 |
+
],
|
| 940 |
+
"mode": "predict",
|
| 941 |
+
"model_type": "STFold",
|
| 942 |
+
"stfold_type": "model_2_ptm",
|
| 943 |
+
"torch_dtype": "float32",
|
| 944 |
+
"transformers_version": "4.31.0.dev0"
|
| 945 |
+
}
|
model_2_ptm/pytorch_model.bin
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:92737473ece460027cce2a9df44d4fae9681c9ebf06f3a660d20713a210b8e94
|
| 3 |
+
size 374784719
|
model_4_ptm/config.json
ADDED
|
@@ -0,0 +1,945 @@
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| 1 |
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| 2 |
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| 3 |
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model_5_ptm/config.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"CONFIG": {
|
| 3 |
+
"data": {
|
| 4 |
+
"transform": {
|
| 5 |
+
"common": {
|
| 6 |
+
"crop_size": {
|
| 7 |
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"eval": null,
|
| 8 |
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"finetune": 384,
|
| 9 |
+
"predict": null,
|
| 10 |
+
"train": 256
|
| 11 |
+
},
|
| 12 |
+
"feats": {
|
| 13 |
+
"aatype": [
|
| 14 |
+
"num residues placeholder"
|
| 15 |
+
],
|
| 16 |
+
"all_atom_mask": [
|
| 17 |
+
"num residues placeholder",
|
| 18 |
+
null
|
| 19 |
+
],
|
| 20 |
+
"all_atom_positions": [
|
| 21 |
+
"num residues placeholder",
|
| 22 |
+
null,
|
| 23 |
+
null
|
| 24 |
+
],
|
| 25 |
+
"alt_chi_angles": [
|
| 26 |
+
"num residues placeholder",
|
| 27 |
+
null
|
| 28 |
+
],
|
| 29 |
+
"assembly_num_chains": [
|
| 30 |
+
null
|
| 31 |
+
],
|
| 32 |
+
"asym_id": [
|
| 33 |
+
"num residues placeholder"
|
| 34 |
+
],
|
| 35 |
+
"asym_len": [
|
| 36 |
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null
|
| 37 |
+
],
|
| 38 |
+
"atom14_alt_gt_exists": [
|
| 39 |
+
"num residues placeholder",
|
| 40 |
+
null
|
| 41 |
+
],
|
| 42 |
+
"atom14_alt_gt_positions": [
|
| 43 |
+
"num residues placeholder",
|
| 44 |
+
null,
|
| 45 |
+
null
|
| 46 |
+
],
|
| 47 |
+
"atom14_atom_exists": [
|
| 48 |
+
"num residues placeholder",
|
| 49 |
+
null
|
| 50 |
+
],
|
| 51 |
+
"atom14_atom_is_ambiguous": [
|
| 52 |
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"num residues placeholder",
|
| 53 |
+
null
|
| 54 |
+
],
|
| 55 |
+
"atom14_gt_exists": [
|
| 56 |
+
"num residues placeholder",
|
| 57 |
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null
|
| 58 |
+
],
|
| 59 |
+
"atom14_gt_positions": [
|
| 60 |
+
"num residues placeholder",
|
| 61 |
+
null,
|
| 62 |
+
null
|
| 63 |
+
],
|
| 64 |
+
"atom37_atom_exists": [
|
| 65 |
+
"num residues placeholder",
|
| 66 |
+
null
|
| 67 |
+
],
|
| 68 |
+
"backbone_rigid_mask": [
|
| 69 |
+
"num residues placeholder"
|
| 70 |
+
],
|
| 71 |
+
"backbone_rigid_tensor": [
|
| 72 |
+
"num residues placeholder",
|
| 73 |
+
null,
|
| 74 |
+
null
|
| 75 |
+
],
|
| 76 |
+
"bert_mask": [
|
| 77 |
+
"msa placeholder",
|
| 78 |
+
"num residues placeholder"
|
| 79 |
+
],
|
| 80 |
+
"chi_angles_sin_cos": [
|
| 81 |
+
"num residues placeholder",
|
| 82 |
+
null,
|
| 83 |
+
null
|
| 84 |
+
],
|
| 85 |
+
"chi_mask": [
|
| 86 |
+
"num residues placeholder",
|
| 87 |
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null
|
| 88 |
+
],
|
| 89 |
+
"cluster_bias_mask": [
|
| 90 |
+
"msa placeholder"
|
| 91 |
+
],
|
| 92 |
+
"entity_id": [
|
| 93 |
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"num residues placeholder"
|
| 94 |
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],
|
| 95 |
+
"extra_deletion_value": [
|
| 96 |
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"extra msa placeholder",
|
| 97 |
+
"num residues placeholder"
|
| 98 |
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],
|
| 99 |
+
"extra_has_deletion": [
|
| 100 |
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"extra msa placeholder",
|
| 101 |
+
"num residues placeholder"
|
| 102 |
+
],
|
| 103 |
+
"extra_msa": [
|
| 104 |
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"extra msa placeholder",
|
| 105 |
+
"num residues placeholder"
|
| 106 |
+
],
|
| 107 |
+
"extra_msa_mask": [
|
| 108 |
+
"extra msa placeholder",
|
| 109 |
+
"num residues placeholder"
|
| 110 |
+
],
|
| 111 |
+
"extra_msa_row_mask": [
|
| 112 |
+
"extra msa placeholder"
|
| 113 |
+
],
|
| 114 |
+
"is_distillation": [],
|
| 115 |
+
"msa_feat": [
|
| 116 |
+
"msa placeholder",
|
| 117 |
+
"num residues placeholder",
|
| 118 |
+
null
|
| 119 |
+
],
|
| 120 |
+
"msa_mask": [
|
| 121 |
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"msa placeholder",
|
| 122 |
+
"num residues placeholder"
|
| 123 |
+
],
|
| 124 |
+
"msa_row_mask": [
|
| 125 |
+
"msa placeholder"
|
| 126 |
+
],
|
| 127 |
+
"no_recycling_iters": [],
|
| 128 |
+
"num_sym": [
|
| 129 |
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"num residues placeholder"
|
| 130 |
+
],
|
| 131 |
+
"pseudo_beta": [
|
| 132 |
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"num residues placeholder",
|
| 133 |
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null
|
| 134 |
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],
|
| 135 |
+
"pseudo_beta_mask": [
|
| 136 |
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"num residues placeholder"
|
| 137 |
+
],
|
| 138 |
+
"residue_index": [
|
| 139 |
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"num residues placeholder"
|
| 140 |
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],
|
| 141 |
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"residx_atom14_to_atom37": [
|
| 142 |
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"num residues placeholder",
|
| 143 |
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null
|
| 144 |
+
],
|
| 145 |
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"residx_atom37_to_atom14": [
|
| 146 |
+
"num residues placeholder",
|
| 147 |
+
null
|
| 148 |
+
],
|
| 149 |
+
"resolution": [],
|
| 150 |
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"rigidgroups_alt_gt_frames": [
|
| 151 |
+
"num residues placeholder",
|
| 152 |
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null,
|
| 153 |
+
null,
|
| 154 |
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null
|
| 155 |
+
],
|
| 156 |
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"rigidgroups_group_exists": [
|
| 157 |
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"num residues placeholder",
|
| 158 |
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null
|
| 159 |
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],
|
| 160 |
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"rigidgroups_group_is_ambiguous": [
|
| 161 |
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"num residues placeholder",
|
| 162 |
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null
|
| 163 |
+
],
|
| 164 |
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"rigidgroups_gt_exists": [
|
| 165 |
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"num residues placeholder",
|
| 166 |
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null
|
| 167 |
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],
|
| 168 |
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"rigidgroups_gt_frames": [
|
| 169 |
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"num residues placeholder",
|
| 170 |
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null,
|
| 171 |
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null,
|
| 172 |
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null
|
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| 915 |
+
"train": 128
|
| 916 |
+
},
|
| 917 |
+
"globals.is_multimer": true,
|
| 918 |
+
"globals.use_templates": true,
|
| 919 |
+
"model.auxiliary_heads.masked_msa_head_c_out": 22,
|
| 920 |
+
"model.auxiliary_heads.tm_enabled": true,
|
| 921 |
+
"model.evoformer_stack.fused": true,
|
| 922 |
+
"model.evoformer_stack.opm_first": true,
|
| 923 |
+
"model.extra_msa_stack.fused": true,
|
| 924 |
+
"model.extra_msa_stack.opm_first": true,
|
| 925 |
+
"model.feature_embedder.c_taf": 34,
|
| 926 |
+
"model.feature_embedder.tf_dim": 21,
|
| 927 |
+
"model.structure_module.ipa_scalar_bias": false,
|
| 928 |
+
"model.structure_module.position_scale": 20,
|
| 929 |
+
"model.structure_module.separate_kv": true,
|
| 930 |
+
"model.template_pair_stack.attention_first": false
|
| 931 |
+
},
|
| 932 |
+
"model_5_ptm": {
|
| 933 |
+
"model.auxiliary_heads.tm_enabled": true
|
| 934 |
+
}
|
| 935 |
+
},
|
| 936 |
+
"_config": null,
|
| 937 |
+
"architectures": [
|
| 938 |
+
"STFold"
|
| 939 |
+
],
|
| 940 |
+
"mode": "predict",
|
| 941 |
+
"model_type": "STFold",
|
| 942 |
+
"stfold_type": "model_5_ptm",
|
| 943 |
+
"torch_dtype": "float32",
|
| 944 |
+
"transformers_version": "4.31.0.dev0"
|
| 945 |
+
}
|
model_5_ptm/pytorch_model.bin
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:e82bbd6632597526420ede893a27c8e980679848c005b0bae887dc8cd30c1c43
|
| 3 |
+
size 373419318
|