{
  "id": 104830,
  "title": "Useful open source libraries",
  "url": "/competitions/champs-scalar-coupling/discussion/104830",
  "author_name": "Jonathan Mailoa",
  "post_date": "2019-08-19T13:11:33.044000",
  "votes": 9,
  "comment_count": 3,
  "views": 0,
  "content": "<p>I thought I'd share some open source chemistry toolkit libraries we have been using to preprocess our molecule data in Python. Hope they're useful, in case you haven't been using them!\n- rdkit: <a href=\"https://www.rdkit.org/\">https://www.rdkit.org/</a>\n- xyz2mol: <a href=\"https://github.com/jensengroup/xyz2mol\">https://github.com/jensengroup/xyz2mol</a> --&gt; a good interface to rdkit\n- openbabel: <a href=\"https://openbabel.org/docs/dev/Installation/install.html\">https://openbabel.org/docs/dev/Installation/install.html</a>\n- pybel: <a href=\"https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html\">https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html</a> --&gt; a good interface to openbabel</p>",
  "messages": [
    {
      "id": 602759,
      "postDate": "2019-08-19T13:11:33.043Z",
      "content": "<p>I thought I'd share some open source chemistry toolkit libraries we have been using to preprocess our molecule data in Python. Hope they're useful, in case you haven't been using them!\n- rdkit: <a href=\"https://www.rdkit.org/\">https://www.rdkit.org/</a>\n- xyz2mol: <a href=\"https://github.com/jensengroup/xyz2mol\">https://github.com/jensengroup/xyz2mol</a> --&gt; a good interface to rdkit\n- openbabel: <a href=\"https://openbabel.org/docs/dev/Installation/install.html\">https://openbabel.org/docs/dev/Installation/install.html</a>\n- pybel: <a href=\"https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html\">https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html</a> --&gt; a good interface to openbabel</p>",
      "rawMarkdown": "I thought I'd share some open source chemistry toolkit libraries we have been using to preprocess our molecule data in Python. Hope they're useful, in case you haven't been using them!\n- rdkit: https://www.rdkit.org/\n- xyz2mol: https://github.com/jensengroup/xyz2mol --&gt; a good interface to rdkit\n- openbabel: https://openbabel.org/docs/dev/Installation/install.html\n- pybel: https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html --&gt; a good interface to openbabel",
      "votes": 9
    },
    {
      "id": 602979,
      "postDate": "2019-08-19T18:04:18.690Z",
      "content": "<p>I am using <a href=\"https://singroup.github.io/dscribe/index.html\">DScribe</a> and <a href=\"http://www.qmlcode.org/qml.html\">QML</a> to generate features to generate ACSF/BoB features for the MPNN and SOAP/LMBTR for Keras NN on the fly using <code>fit_generator</code>, both of which produce little overhead.</p>",
      "rawMarkdown": "I am using [DScribe](https://singroup.github.io/dscribe/index.html) and [QML](http://www.qmlcode.org/qml.html) to generate features to generate ACSF/BoB features for the MPNN and SOAP/LMBTR for Keras NN on the fly using `fit_generator`, both of which produce little overhead.",
      "votes": 1
    },
    {
      "id": 602961,
      "postDate": "2019-08-19T17:32:35.950Z",
      "rawMarkdown": "",
      "isDeleted": true
    },
    {
      "id": 604573,
      "postDate": "2019-08-21T14:35:39.867Z",
      "content": "<p>Thanks!</p>",
      "rawMarkdown": "Thanks!"
    }
  ],
  "comments": [
    {
      "id": 602979,
      "author_name": "Shuhao Cao",
      "author_url": "",
      "post_date": "2019-08-19T18:04:18.690000",
      "content": "<p>I am using <a href=\"https://singroup.github.io/dscribe/index.html\">DScribe</a> and <a href=\"http://www.qmlcode.org/qml.html\">QML</a> to generate features to generate ACSF/BoB features for the MPNN and SOAP/LMBTR for Keras NN on the fly using <code>fit_generator</code>, both of which produce little overhead.</p>",
      "votes": 1,
      "replies": []
    },
    {
      "id": 602961,
      "author_name": "",
      "author_url": "",
      "post_date": "2019-08-19T17:32:35.950000",
      "content": "",
      "votes": 0,
      "replies": []
    },
    {
      "id": 604573,
      "author_name": "Den Shy",
      "author_url": "",
      "post_date": "2019-08-21T14:35:39.867000",
      "content": "<p>Thanks!</p>",
      "votes": 0,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "602759": "I thought I'd share some open source chemistry toolkit libraries we have been using to preprocess our molecule data in Python. Hope they're useful, in case you haven't been using them!\n- rdkit: https://www.rdkit.org/\n- xyz2mol: https://github.com/jensengroup/xyz2mol --&gt; a good interface to rdkit\n- openbabel: https://openbabel.org/docs/dev/Installation/install.html\n- pybel: https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html --&gt; a good interface to openbabel",
    "602979": "I am using [DScribe](https://singroup.github.io/dscribe/index.html) and [QML](http://www.qmlcode.org/qml.html) to generate features to generate ACSF/BoB features for the MPNN and SOAP/LMBTR for Keras NN on the fly using `fit_generator`, both of which produce little overhead.",
    "602961": "",
    "604573": "Thanks!"
  }
}