Chem_Faiss_Colab.ipynb

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  "metadata": {
    "colab": {
      "name": "Chem_Faiss_Colab.ipynb",
      "provenance": [],
      "authorship_tag": "ABX9TyPLkI0WeF29aKZpnZitpL8l",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/ritabratamaiti/Chem-Faiss/blob/master/Chem_Faiss_Colab.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "H1WWe-0KsNzu",
        "colab_type": "text"
      },
      "source": [
        "Get the Chem Faiss Project from Github."
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "dV9BYTyQrIc-",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 118
        },
        "outputId": "9b8e19d8-b370-42f7-d8a9-04cd726ecf2c"
      },
      "source": [
        "!git clone https://github.com/ritabratamaiti/Chem-Faiss\n",
        "!mv /content/Chem-Faiss/* /content/"
      ],
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "Cloning into 'Chem-Faiss'...\n",
            "remote: Enumerating objects: 65, done.\u001b[K\n",
            "remote: Counting objects: 100% (65/65), done.\u001b[K\n",
            "remote: Compressing objects: 100% (65/65), done.\u001b[K\n",
            "remote: Total 65 (delta 25), reused 0 (delta 0), pack-reused 0\u001b[K\n",
            "Unpacking objects: 100% (65/65), done.\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "Lgnlw3qosg47",
        "colab_type": "text"
      },
      "source": [
        "Install RDKit and Faiss"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "3sfl6XMZrOyT",
        "colab_type": "code",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 1000
        },
        "outputId": "79591763-3a41-4cce-8ee2-4aa4aac1fae3"
      },
      "source": [
        "!wget https://anaconda.org/pytorch/faiss-gpu/1.2.1/download/linux-64/faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2\n",
        "!tar xvjf faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2\n",
        "!cp -r lib/python3.6/site-packages/* /usr/local/lib/python3.6/dist-packages/\n",
        "!pip install mkl\n",
        "!wget https://anaconda.org/rdkit/rdkit/2018.09.1.0/download/linux-64/rdkit-2018.09.1.0-py36h71b666b_1.tar.bz2 -O rdkit.tar.bz2 -q\n",
        "!mkdir rdkit\n",
        "!tar xjf rdkit.tar.bz2 -C rdkit\n",
        "!cp -r rdkit/lib/python3.6/site-packages/* /usr/local/lib/python3.6/dist-packages/\n",
        "!cp -r rdkit/lib/*.so.* /usr/lib/x86_64-linux-gnu/\n",
        "!ln -s /usr/lib/x86_64-linux-gnu/libboost_python3-py36.so.1.65.1 /usr/lib/x86_64-linux-gnu/libboost_python3.so.1.65.1"
      ],
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "text": [
            "--2020-05-27 20:22:32--  https://anaconda.org/pytorch/faiss-gpu/1.2.1/download/linux-64/faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2\n",
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            "Connecting to anaconda.org (anaconda.org)|104.17.92.24|:443... connected.\n",
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            "--2020-05-27 20:22:33--  https://binstar-cio-packages-prod.s3.amazonaws.com/5a15c9cc393ec612061f033a/5ac54beae586bb11ec0ace46?response-content-disposition=attachment%3B%20filename%3D%22faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2%22%3B%20filename%2A%3DUTF-8%27%27faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2&response-content-type=application%2Fx-tar&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Expires=60&X-Amz-Date=20200527T202233Z&X-Amz-SignedHeaders=host&X-Amz-Security-Token=IQoJb3JpZ2luX2VjEGcaCXVzLWVhc3QtMSJGMEQCID4GchqbOVla4pamqkbX994joW%2FixUfz%2FTv5gy72gDKZAiBslpEONlxH5rBDpPG70r3cE7xqJTwt5iXccvQjCAH98yq9AwjA%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F8BEAAaDDQ1NTg2NDA5ODM3OCIMEUDOQ1b6b08fFoESKpED4aTbI0FGcQHDkz%2BtzQ8DEjz%2B99lNMTNm6B3yqv2Ae5PiU1ISz%2BTZILuzrl1kydfXnH00QEvXxpeByeXzYH0HsRnM2RjNEDGqe%2Fcthvw%2BOyQfQ8uTi0fSyURTuTIllG0ZGhDY4r3kw5XZBUlZIEWZoUvhdK2F4C6RwLwZwLbnmRV2uql9H9N4bPIY%2FpDucSinFaUvt8Lh63hMDntVF94QPI8TGktEnvlYLBMOcKVwDMdZRf7rzLnUjmpvJkFxoVofgbsKV%2F7rhipP8vi%2Fz1eoMpGV91h7%2BFJC5ZujqHvcRGxa1T2t9Snf5QX8PyDwySF%2FfhNqEL6IJKKqY6k6rC8N6z3TS8eYfZi7H4BBE%2Bil%2BwJO4unLV%2BGz1ld9M3g%2BeG7n42R4C6VuEerExe01UUaEMebDEYn3o3CZGjraEku7vvI6V8H1fXtGiyAhwKMd4e5PTd4RtUCVdhtFb8Tzn5NoRq47%2F99LeHOdnOpmonUjgXd0qGuwdzAQ81%2FPwlimZbFMmb3xik0sEEE0dQ7Andjq0GMwlPW59gU67AHdcPcrowuzn%2BSMYuf5w122Qkmhd%2Fe8ThgUVonkyoGHdBBgi8UO0Y4S5HXAnQQ0JkNwb4e2a9cU3a9o%2FZSgWmdtXAxxgrXIBn774VTVAICRr2obMEGBIqhhtStrJ2pLfEOEfQK9MNx7XtxWGAmjZ6RkeXZK4iZv4JlguFOkHez5kSq3fnq9mcDdv5d%2F8He%2B2T1TzxQd0a67dEKiHpAjc6GK0SPCTTXZ37vCjm4C0fzJPWQZ7GOaUez7F2tUvvUWXts4tzYAWO6usDMdinBsp6hNLhTfXY%2B%2B%2F2HD0M4KDZJMo%2B6Jl6NDp%2FbxitOrqw%3D%3D&X-Amz-Credential=ASIAWUI46DZFHZLUBKAR%2F20200527%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=9d2dcd28efd603b840df442aacd3946e7170fd8f27e513d1b0275167869e84d2\n",
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            "Length: 25115678 (24M) [application/x-tar]\n",
            "Saving to: ‘faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2’\n",
            "\n",
            "faiss-gpu-1.2.1-py3 100%[===================>]  23.95M  9.36MB/s    in 2.6s    \n",
            "\n",
            "2020-05-27 20:22:37 (9.36 MB/s) - ‘faiss-gpu-1.2.1-py36_cuda9.0.176_1.tar.bz2’ saved [25115678/25115678]\n",
            "\n",
            "info/hash_input.json\n",
            "info/has_prefix\n",
            "info/index.json\n",
            "info/files\n",
            "info/LICENSE.txt\n",
            "info/about.json\n",
            "info/paths.json\n",
            "info/git\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/dependency_links.txt\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/not-zip-safe\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/requires.txt\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/top_level.txt\n",
            "info/test/run_test.py\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/native_libs.txt\n",
            "info/test/run_test.sh\n",
            "info/test/tests/run_tests.sh\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/SOURCES.txt\n",
            "info/recipe/conda_build_config.yaml\n",
            "info/recipe/build.sh\n",
            "info/test/tests/CMakeLists.txt\n",
            "info/test/tests/Makefile\n",
            "info/recipe/meta.yaml.template\n",
            "lib/python3.6/site-packages/faiss-0.1-py3.6.egg-info/PKG-INFO\n",
            "info/test/tests/test_factory.py\n",
            "info/test/tests/test_ivfpq_codec.cpp\n",
            "info/recipe/meta.yaml\n",
            "info/recipe/setup.py\n",
            "info/test/tests/test_blas.cpp\n",
            "info/recipe/makefile.inc\n",
            "info/test/tests/test_ivfpq_indexing.cpp\n",
            "info/test/tests/test_ondisk_ivf.cpp\n",
            "info/test/tests/test_build_blocks.py\n",
            "info/test/tests/test_merge.cpp\n",
            "info/test/tests/test_pairs_decoding.cpp\n",
            "info/test/tests/test_index_composite.py\n",
            "lib/python3.6/site-packages/faiss/__init__.py\n",
            "lib/python3.6/site-packages/faiss/__pycache__/__init__.cpython-36.pyc\n",
            "info/test/tests/test_index.py\n",
            "info/test/tests/test_blas\n",
            "lib/python3.6/site-packages/faiss/__pycache__/swigfaiss.cpython-36.pyc\n",
            "lib/python3.6/site-packages/faiss/swigfaiss.py\n",
            "lib/python3.6/site-packages/faiss/__pycache__/swigfaiss_gpu.cpython-36.pyc\n",
            "lib/python3.6/site-packages/faiss/swigfaiss_gpu.py\n",
            "lib/python3.6/site-packages/faiss/_swigfaiss.so\n",
            "lib/python3.6/site-packages/faiss/_swigfaiss_gpu.so\n",
            "Requirement already satisfied: mkl in /usr/local/lib/python3.6/dist-packages (2019.0)\n",
            "Requirement already satisfied: intel-openmp in /usr/local/lib/python3.6/dist-packages (from mkl) (2020.0.133)\n"
          ],
          "name": "stdout"
        }
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "pcdqbjwftfTK",
        "colab_type": "text"
      },
      "source": [
        "Import Chem Faiss"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "s71cM0ntsKvl",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        "from Chem_Faiss import pipeline\n",
        "import Chem_Faiss"
      ],
      "execution_count": 0,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "ALRZ3qgutls2",
        "colab_type": "text"
      },
      "source": [
        "Your Code Here!"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "iDMOitYqspRp",
        "colab_type": "code",
        "colab": {}
      },
      "source": [
        ""
      ],
      "execution_count": 0,
      "outputs": []
    }
  ]
}