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Commit 08276f0f authored by jnwei's avatar jnwei Committed by Jennifer
Browse files

Updates commit value for OpenFold notebook.

parent eb4d1e57
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Showing with 47 additions and 16 deletions
notebooks/OpenFold.ipynb
View file @ 08276f0f
{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github"
},
"source": [
"<a href=\"https://colab.research.google.com/github/aqlaboratory/openfold/blob/main/notebooks/OpenFold.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "markdown",
"metadata": {
......@@ -51,9 +42,21 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "rowN0bVYLe9n"
"id": "rowN0bVYLe9n",
"outputId": "a947f86a-e860-44e6-eb51-81c26608fdfc",
"colab": {
"base_uri": "https://localhost:8080/"
}
},
"outputs": [],
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Length of input sequence : 136\n"
]
}
],
"source": [
"#@markdown ### Enter the amino acid sequence to fold ⬇️\n",
"#@markdown For multiple sequences, separate sequences with a colon `:`\n",
......@@ -136,7 +139,7 @@
"\n",
" %shell mkdir -p /content/openfold/openfold/resources\n",
"\n",
" commit = \"e2e19f16676b1a409f9ba3a6f69b11ee7f5887c2\"\n",
" commit = \"a96ffd67f8c96f8c4decc3abdd2cffbb57fc5764\"\n",
" os.system(f\"pip install -q git+https://github.com/aqlaboratory/openfold.git@{commit}\")\n",
"\n",
" os.system(f\"cp -f -p /content/stereo_chemical_props.txt /usr/local/lib/python{python_version}/site-packages/openfold/resources/\")\n",
......@@ -198,9 +201,37 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"id": "_FpxxMo-mvcP"
"id": "_FpxxMo-mvcP",
"outputId": "e6d601db-0945-4091-91a1-2aba04ebeba7",
"colab": {
"base_uri": "https://localhost:8080/",
"height": 492
}
},
"outputs": [],
"outputs": [
{
"output_type": "stream",
"name": "stderr",
"text": [
"/usr/local/lib/python3.10/site-packages/openfold/data/templates.py:86: FutureWarning: In the future `np.object` will be defined as the corresponding NumPy scalar.\n",
" \"template_domain_names\": np.object,\n"
]
},
{
"output_type": "error",
"ename": "AttributeError",
"evalue": "module 'numpy' has no attribute 'object'.\n`np.object` was a deprecated alias for the builtin `object`. To avoid this error in existing code, use `object` by itself. Doing this will not modify any behavior and is safe. \nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-6-24dea6794813>\u001b[0m in \u001b[0;36m<cell line: 50>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mfeature_pipeline\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 49\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mparsers\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 50\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdata_pipeline\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 51\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mmsa_pairing\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 52\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mfeature_processing_multimer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.10/site-packages/openfold/data/data_pipeline.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 27\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mpickle\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 28\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mtemplates\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mparsers\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmmcif_parsing\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmsa_identifiers\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmsa_pairing\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfeature_processing_multimer\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 29\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtemplates\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mget_custom_template_features\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mempty_template_feats\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 30\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mopenfold\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtools\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mjackhmmer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhhblits\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhhsearch\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhmmsearch\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.10/site-packages/openfold/data/templates.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 84\u001b[0m \u001b[0;34m\"template_all_atom_mask\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfloat32\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 85\u001b[0m \u001b[0;34m\"template_all_atom_positions\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfloat32\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 86\u001b[0;31m \u001b[0;34m\"template_domain_names\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobject\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 87\u001b[0m \u001b[0;34m\"template_sequence\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mobject\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 88\u001b[0m \u001b[0;34m\"template_sum_probs\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfloat32\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.10/dist-packages/numpy/__init__.py\u001b[0m in \u001b[0;36m__getattr__\u001b[0;34m(attr)\u001b[0m\n\u001b[1;32m 317\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 318\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mattr\u001b[0m \u001b[0;32min\u001b[0m \u001b[0m__former_attrs__\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 319\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mAttributeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m__former_attrs__\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mattr\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 320\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 321\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mattr\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'testing'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mAttributeError\u001b[0m: module 'numpy' has no attribute 'object'.\n`np.object` was a deprecated alias for the builtin `object`. To avoid this error in existing code, use `object` by itself. Doing this will not modify any behavior and is safe. \nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations"
]
}
],
"source": [
"#@title Import Python packages\n",
"#@markdown Please execute this cell by pressing the *Play* button on\n",
......@@ -259,7 +290,7 @@
"from openfold.np import protein\n",
"from openfold.np.relax import relax\n",
"from openfold.np.relax.utils import overwrite_b_factors\n",
"from openfold.utils.import_weights import import_jax_weights_\n",
"from openfold.utils.import_weights import import_jax_weights_, import_openfold_weights_\n",
"from openfold.utils.tensor_utils import tensor_tree_map\n",
"\n",
"from IPython import display\n",
......@@ -582,7 +613,7 @@
" model_name,\n",
" )\n",
" d = torch.load(params_name)\n",
" openfold_model.load_state_dict(d)\n",
" import_openfold_weights_(model=openfold_model, state_dict=d)\n",
" else:\n",
" raise ValueError(f\"Invalid weight set: {weight_set}\")\n",
"\n",
......
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