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Fixed JAX Tree error #5

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Fixed JAX Tree error #5

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9336c5b
Fixed JAX Tree error
AtharvaTilewale Nov 11, 2025
7398492
Fixed all JAX Tree errors
AtharvaTilewale Nov 11, 2025
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40 changes: 20 additions & 20 deletions af2bind.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
"colab_type": "text",
"id": "view-in-github"
},
"source": [
"<a href=\"https://colab.research.google.com/github/sokrypton/af2bind/blob/main/af2bind.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
Expand Down Expand Up @@ -123,7 +123,7 @@
" with open(f\"af2bind_params/attempt_7_2k_lam0-03/{model_type}.pickle\",\"rb\") as handle:\n",
" params_ = pickle.load(handle)\n",
" params_ = dict(**params_[\"~\"], **params_[\"linear\"])\n",
" p = jax.tree_map(lambda x:np.asarray(x), params_)\n",
" p = jax.tree.map(lambda x:np.asarray(x), params_)\n",
"\n",
" # get predictions\n",
" x = (x - p[\"mean\"]) / p[\"std\"]\n",
Expand All @@ -135,6 +135,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"cellView": "form",
"id": "5r6hHIimktMH"
},
"outputs": [],
"source": [
"#@title **Run AF2BIND** 🔬\n",
"target_pdb = \"6w70\" #@param {type:\"string\"}\n",
Expand Down Expand Up @@ -201,13 +207,7 @@
"\n",
"print(\"\\n🧪Pymol Selection Cmd:\")\n",
"print(pymol_cmd)"
],
"metadata": {
"cellView": "form",
"id": "5r6hHIimktMH"
},
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
Expand Down Expand Up @@ -327,6 +327,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"cellView": "form",
"id": "6LNbani6bCiz"
},
"outputs": [],
"source": [
"#@title **Activation analysis** (optional)\n",
"pbind_cutoff = 0.5 # @param [\"0.0\", \"0.5\", \"0.9\"] {type:\"raw\"}\n",
Expand All @@ -350,20 +356,14 @@
" color_continuous_scale=[\"red\", \"white\", \"blue\"],\n",
" )\n",
"fig.show()"
],
"metadata": {
"cellView": "form",
"id": "6LNbani6bCiz"
},
"execution_count": null,
"outputs": []
]
}
],
"metadata": {
"accelerator": "GPU",
"colab": {
"provenance": [],
"include_colab_link": true
"include_colab_link": true,
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
Expand All @@ -375,4 +375,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
40 changes: 20 additions & 20 deletions af2bind_experimental.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
"colab_type": "text",
"id": "view-in-github"
},
"source": [
"<a href=\"https://colab.research.google.com/github/sokrypton/af2bind/blob/main/af2bind_experimental.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
Expand Down Expand Up @@ -118,7 +118,7 @@
" with open(f\"af2bind_params/attempt_7_2k_lam0-03/{model_type}.pickle\",\"rb\") as handle:\n",
" params_ = pickle.load(handle)\n",
" params_ = dict(**params_[\"~\"], **params_[\"linear\"])\n",
" p = jax.tree_map(lambda x:np.asarray(x), params_)\n",
" p = jax.tree.map(lambda x:np.asarray(x), params_)\n",
"\n",
" # get predictions\n",
" x = (x - p[\"mean\"]) / p[\"std\"]\n",
Expand All @@ -130,6 +130,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"cellView": "form",
"id": "5r6hHIimktMH"
},
"outputs": [],
"source": [
"#@title **Run AF2BIND** 🔬\n",
"target_pdb = \"6w70\" #@param {type:\"string\"}\n",
Expand Down Expand Up @@ -227,13 +233,7 @@
"\n",
"print(\"\\n🧪Pymol Selection Cmd:\")\n",
"print(pymol_cmd)"
],
"metadata": {
"cellView": "form",
"id": "5r6hHIimktMH"
},
"execution_count": null,
"outputs": []
]
},
{
"cell_type": "code",
Expand Down Expand Up @@ -353,6 +353,12 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"cellView": "form",
"id": "6LNbani6bCiz"
},
"outputs": [],
"source": [
"#@title **Activation analysis** (optional)\n",
"pbind_cutoff = 0.5 # @param [\"0.0\", \"0.5\", \"0.9\"] {type:\"raw\"}\n",
Expand All @@ -376,20 +382,14 @@
" color_continuous_scale=[\"red\", \"white\", \"blue\"],\n",
" )\n",
"fig.show()"
],
"metadata": {
"cellView": "form",
"id": "6LNbani6bCiz"
},
"execution_count": null,
"outputs": []
]
}
],
"metadata": {
"accelerator": "GPU",
"colab": {
"provenance": [],
"include_colab_link": true
"include_colab_link": true,
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
Expand All @@ -401,4 +401,4 @@
},
"nbformat": 4,
"nbformat_minor": 0
}
}
2 changes: 1 addition & 1 deletion af2bind_large_pdb.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@
" with open(f\"af2bind_params/attempt_7_2k_lam0-03/{model_type}.pickle\",\"rb\") as handle:\n",
" params_ = pickle.load(handle)\n",
" params_ = dict(**params_[\"~\"], **params_[\"linear\"])\n",
" p = jax.tree_map(lambda x:np.asarray(x), params_)\n",
" p = jax.tree.map(lambda x:np.asarray(x), params_) # Changed jax.tree_map to jax.tree.map\n",
"\n",
" # get predictions\n",
" x = (x - p[\"mean\"]) / p[\"std\"]\n",
Expand Down