From 35e9ec9e2e011f8d8fc433179f3f885c4fa6f202 Mon Sep 17 00:00:00 2001 From: John Peters Date: Tue, 27 Aug 2024 13:38:14 -0500 Subject: [PATCH] "Removed login from colab notebook" --- notebooks/colab_predicting.ipynb | 1904 ++++++------------------------ 1 file changed, 390 insertions(+), 1514 deletions(-) diff --git a/notebooks/colab_predicting.ipynb b/notebooks/colab_predicting.ipynb index 203a60e..8141ebe 100644 --- a/notebooks/colab_predicting.ipynb +++ b/notebooks/colab_predicting.ipynb @@ -15,7 +15,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 15, "metadata": { "cellView": "form", "id": "WkNKKIqXr4OU" @@ -28,30 +28,30 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 16, "metadata": { "cellView": "form", "colab": { "base_uri": "https://localhost:8080/" }, "id": "tP_HrR5YSiqk", - "outputId": "c4f0a814-5daf-45b1-8d7f-cb7fbbbb3142" + "outputId": "70aa2f54-639d-4406-a0ce-6557caaa17d2" }, "outputs": [ { - "name": "stdout", "output_type": "stream", + "name": "stdout", "text": [ - "--2024-08-23 20:50:43-- https://raw.githubusercontent.com/gitter-lab/metl-pretrained/main/pdbs/2qmt_p.pdb\n", + "--2024-08-27 18:37:23-- https://raw.githubusercontent.com/gitter-lab/metl-pretrained/main/pdbs/2qmt_p.pdb\n", "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...\n", "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 78764 (77K) [text/plain]\n", "Saving to: ‘2qmt_p.pdb’\n", "\n", - "\r2qmt_p.pdb 0%[ ] 0 --.-KB/s \r2qmt_p.pdb 100%[===================>] 76.92K --.-KB/s in 0.009s \n", + "\r2qmt_p.pdb 0%[ ] 0 --.-KB/s \r2qmt_p.pdb 100%[===================>] 76.92K --.-KB/s in 0.01s \n", "\n", - "2024-08-23 20:50:43 (8.73 MB/s) - ‘2qmt_p.pdb’ saved [78764/78764]\n", + "2024-08-27 18:37:23 (6.32 MB/s) - ‘2qmt_p.pdb’ saved [78764/78764]\n", "\n" ] } @@ -63,7 +63,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 17, "metadata": { "cellView": "form", "id": "mpjvGjzArLF1" @@ -114,105 +114,12 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 18, "metadata": { "cellView": "form", - "colab": { - "base_uri": "https://localhost:8080/", - "height": 202, - "referenced_widgets": [ - "0e89a61715a2405795e9204d487e16a7", - "706504f4e2b44623b06d81e4bfb9fec6", - "6139b052d48b4b8a88bf1d0cfbee89d1", - "cb8a74409964470399e759c9c373c1fb", - "1127b0a462414b60937c6f38b1adee12", - "fc53173bf32d4afabfdf9ee50cb3b00a", - "eb4407c45c0e4ac9b0fed9b2e0c56ff9", - "b31c4d8d76224754846690925ecf8910", - "554bd3d19ad24ab79e011fe89c768793", - "b292e0907116481f8a67236d5fff4023", - "948b99490be74d4483ce432455905bda", - "9a4fa89166dc4ed9ba241082e0b295d0", - "e89279b489fc4dcaa507ff5b8e67d890", - "5268bf3171724c6aabba1a5e491120d0", - "174d3daccf6542128f9e665d225da25f", - "49c094a124f6497f81e8d99d5f539c3e", - "aceb1c83343f42f5ba327ea0181f54ba", - "3f8c6dc919de4ca79ac2d5bb4cac2d4f", - "279615cb9a9f4d0a939e915aadb1390b", - "706b2fd4323d42129ef68cf138535fe8", - "26ba5323b65441d5ae3bca32edeaeb6b", - "eb142d0f070c47a19b80d327c79929db", - "3db12ffb0cc64e47a9445ed6f30ad4a7", - "c064486920084853839ba97bbf7adcef", - "c48bf3a44113463e9a2ce990ca58fd89", - "49ed05570a474155ac1cc9c920956277", - "b8de008d9ea8492d89b4220190f341df", - "561825fd86a24139b76b0714fcf4ee07", - "e243c6dbff6f462ba643e44ad05d6199", - "dca0f426047a4fc69905113bfab76ddf", - "61459277623143eeae90e152128d8e41", - "0cff14529ed44602992665ab2769cc3a", - "840350d162c54b248ad178915821d3e2" - ] - }, - "id": "vIp69-KLrLF8", - "outputId": "0a5081fe-d8ae-45cb-ab38-0352ccb33fcd" + "id": "vIp69-KLrLF8" }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The token has not been saved to the git credentials helper. Pass `add_to_git_credential=True` in this function directly or `--add-to-git-credential` if using via `huggingface-cli` if you want to set the git credential as well.\n", - "Token is valid (permission: write).\n", - "Your token has been saved to /root/.cache/huggingface/token\n", - "Login successful\n" - ] - }, - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "0e89a61715a2405795e9204d487e16a7", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [ - "config.json: 0%| | 0.00/269 [00:00" + ], "text/html": [ "\n", "\n" - ], - "text/plain": [ - "" ] }, - "metadata": {}, - "output_type": "display_data" + "metadata": {} }, { + "output_type": "display_data", "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "652003f6d3774d4f96dccccc6531d9c2", - "version_major": 2, - "version_minor": 0 - }, "text/plain": [ "Textarea(value='', description='Variant String:', layout=Layout(height='100px', width='500px'), placeholder='[…" - ] + ], + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 0, + "model_id": "2e1b8d20f17b4ef584c853fd4a99bf4b" + } }, - "metadata": {}, - "output_type": "display_data" + "metadata": {} } ], "source": [ @@ -460,35 +360,35 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 23, "metadata": { "cellView": "form", "colab": { "base_uri": "https://localhost:8080/", "height": 49, "referenced_widgets": [ - "f77f31e709c84c48b86316dbe9d7b0c9", - "bd9755e9b09148d480b2d4604aa9ff16", - "3171d7d717ba4baba7ac948a4fb60529" + "18ee47ab60e047bd8881c70e1999438f", + "5ddecf2c18394ec2bda2e38999d2b1ae", + "429005aabdfa4724af48b83a45bf1868" ] }, "id": "8TLYi6orHN_8", - "outputId": "adaa8601-177c-4281-cc09-fd486828b577" + "outputId": "e9b214fa-534f-4088-df0b-49ab6d6da89f" }, "outputs": [ { + "output_type": "display_data", "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "f77f31e709c84c48b86316dbe9d7b0c9", - "version_major": 2, - "version_minor": 0 - }, "text/plain": [ "FileUpload(value={}, accept='.json, .txt', description='Upload')" - ] + ], + "application/vnd.jupyter.widget-view+json": { + "version_major": 2, + "version_minor": 0, + "model_id": "18ee47ab60e047bd8881c70e1999438f" + } }, - "metadata": {}, - "output_type": "display_data" + "metadata": {} } ], "source": [ @@ -515,19 +415,19 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 24, "metadata": { "cellView": "form", "colab": { "base_uri": "https://localhost:8080/" }, "id": "mASfltPUrLGI", - "outputId": "bf78aa81-176f-4c65-d311-d128e77c1b2a" + "outputId": "36dba643-0610-4632-d446-2df66c9bf99c" }, "outputs": [ { - "name": "stdout", "output_type": "stream", + "name": "stdout", "text": [ "Using variant placeholder\n" ] @@ -559,7 +459,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 25, "metadata": { "cellView": "form", "id": "ecLAU9IOrLGK" @@ -584,7 +484,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 26, "metadata": { "cellView": "form", "id": "th1JyojWrLGN" @@ -625,29 +525,31 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 27, "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 300 }, "id": "J5XJ-4memIYp", - 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