{
  "id": 105422,
  "title": "Molecule Bond EDA",
  "url": "/competitions/champs-scalar-coupling/discussion/105422",
  "author_name": "",
  "post_date": "2019-08-23T03:13:24.899879900Z",
  "votes": 8,
  "comment_count": 1,
  "views": 0,
  "content": "<p>I updated my Molecule Animation kernel/notebook <a href=\"https://www.kaggle.com/cdeotte/molecule-animations\">here</a> to draw the bonds in the animation. In code cell block 4, there are two variables </p>\n\n<pre><code>BTYPE = '1JHN'\nDISPLAY_BONDS = False\n</code></pre>\n\n<p>You can view different couplings besides <code>1JHC</code> by changing the first variable, and you can add bonds to the animations by changing the second variable. Below I show examples of <code>BTYPE = 2JHN</code> and <code>DISPLAY_BONDS = True</code>.</p>\n\n<p>If you change those variables and run the kernel, it will display 10 examples from small <code>sc_constant</code> to large <code>sc_constant</code> of the type desired. If you wish to display specific bonds of your choice, call the function <code>animate(j, title='', display_bonds=DISPLAY_BONDS)</code>. Set the variable <code>j = train.index[k]</code> for some bond number <code>k</code>.</p>\n\n<p>Afterward hydrogen is positioned at (0,0,0) and nitrogen (the other atom in coupling) is positioned at (1,0,0). Then the molecule is rotated around the x-axis. By viewing different molecules, you will notice that when coupling atoms connect to a ring of atoms, <code>sc_constant</code> is large and when they connect to a non-ring, <code>sc_constant</code> is small. Therefore detecting rings is helpful.</p>\n\n<p><img src=\"http://playagricola.com/Kaggle/b482119.gif\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/b582119.gif\" alt=\"image\"></p>\n\n<p>Since this coupling is <code>2JHN</code> there is always 1 atom between the hydrogen and nitrogen. Most often it is carbon. But 1% of the time it is oxygen and 2% of the time it is another nitrogen. When it is oxygen, <code>sc_constant</code> is small because oxygen has 2 valence and won't make a ring. When it is another nitrogen it likes to make a ring and <code>sc_constant</code> is larger.\n<img src=\"http://playagricola.com/Kaggle/pie82119.png\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/b382119.gif\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/b282119.gif\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/hist82119.png\" alt=\"image\"></p>",
  "messages": [
    {
      "id": "605971",
      "postDate": "08/23/2019 03:13:24",
      "content": "<p>I updated my Molecule Animation kernel/notebook <a href=\"https://www.kaggle.com/cdeotte/molecule-animations\">here</a> to draw the bonds in the animation. In code cell block 4, there are two variables </p>\n\n<pre><code>BTYPE = '1JHN'\nDISPLAY_BONDS = False\n</code></pre>\n\n<p>You can view different couplings besides <code>1JHC</code> by changing the first variable, and you can add bonds to the animations by changing the second variable. Below I show examples of <code>BTYPE = 2JHN</code> and <code>DISPLAY_BONDS = True</code>.</p>\n\n<p>If you change those variables and run the kernel, it will display 10 examples from small <code>sc_constant</code> to large <code>sc_constant</code> of the type desired. If you wish to display specific bonds of your choice, call the function <code>animate(j, title='', display_bonds=DISPLAY_BONDS)</code>. Set the variable <code>j = train.index[k]</code> for some bond number <code>k</code>.</p>\n\n<p>Afterward hydrogen is positioned at (0,0,0) and nitrogen (the other atom in coupling) is positioned at (1,0,0). Then the molecule is rotated around the x-axis. By viewing different molecules, you will notice that when coupling atoms connect to a ring of atoms, <code>sc_constant</code> is large and when they connect to a non-ring, <code>sc_constant</code> is small. Therefore detecting rings is helpful.</p>\n\n<p><img src=\"http://playagricola.com/Kaggle/b482119.gif\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/b582119.gif\" alt=\"image\"></p>\n\n<p>Since this coupling is <code>2JHN</code> there is always 1 atom between the hydrogen and nitrogen. Most often it is carbon. But 1% of the time it is oxygen and 2% of the time it is another nitrogen. When it is oxygen, <code>sc_constant</code> is small because oxygen has 2 valence and won't make a ring. When it is another nitrogen it likes to make a ring and <code>sc_constant</code> is larger.\n<img src=\"http://playagricola.com/Kaggle/pie82119.png\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/b382119.gif\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/b282119.gif\" alt=\"image\">\n<img src=\"http://playagricola.com/Kaggle/hist82119.png\" alt=\"image\"></p>",
      "rawMarkdown": "I updated my Molecule Animation kernel/notebook [here][1] to draw the bonds in the animation. In code cell block 4, there are two variables \n\n    BTYPE = '1JHN'\n    DISPLAY_BONDS = False\n\nYou can view different couplings besides `1JHC` by changing the first variable, and you can add bonds to the animations by changing the second variable. Below I show examples of `BTYPE = 2JHN` and `DISPLAY_BONDS = True`.\n\nIf you change those variables and run the kernel, it will display 10 examples from small `sc_constant` to large `sc_constant` of the type desired. If you wish to display specific bonds of your choice, call the function `animate(j, title='', display_bonds=DISPLAY_BONDS)`. Set the variable `j = train.index[k]` for some bond number `k`.\n\nAfterward hydrogen is positioned at (0,0,0) and nitrogen (the other atom in coupling) is positioned at (1,0,0). Then the molecule is rotated around the x-axis. By viewing different molecules, you will notice that when coupling atoms connect to a ring of atoms, `sc_constant` is large and when they connect to a non-ring, `sc_constant` is small. Therefore detecting rings is helpful.\n\n![image](http://playagricola.com/Kaggle/b482119.gif)\n![image](http://playagricola.com/Kaggle/b582119.gif)\n\nSince this coupling is `2JHN` there is always 1 atom between the hydrogen and nitrogen. Most often it is carbon. But 1% of the time it is oxygen and 2% of the time it is another nitrogen. When it is oxygen, `sc_constant` is small because oxygen has 2 valence and won't make a ring. When it is another nitrogen it likes to make a ring and `sc_constant` is larger.\n![image](http://playagricola.com/Kaggle/pie82119.png)\n![image](http://playagricola.com/Kaggle/b382119.gif)\n![image](http://playagricola.com/Kaggle/b282119.gif)\n![image](http://playagricola.com/Kaggle/hist82119.png)\n\n[1]: https://www.kaggle.com/cdeotte/molecule-animations",
      "votes": null
    },
    {
      "id": "606031",
      "postDate": "08/23/2019 05:26:23",
      "content": "<p>You are Amazing with Molecular Theory...!! <a href=\"/cdeotte\">@cdeotte</a> </p>",
      "rawMarkdown": "You are Amazing with Molecular Theory...!! @cdeotte",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 606031,
      "author_name": "veeralakrishna",
      "author_url": "",
      "post_date": "08/23/2019 05:26:23",
      "content": "<p>You are Amazing with Molecular Theory...!! <a href=\"/cdeotte\">@cdeotte</a> </p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "605971": "I updated my Molecule Animation kernel/notebook [here][1] to draw the bonds in the animation. In code cell block 4, there are two variables \n\n    BTYPE = '1JHN'\n    DISPLAY_BONDS = False\n\nYou can view different couplings besides `1JHC` by changing the first variable, and you can add bonds to the animations by changing the second variable. Below I show examples of `BTYPE = 2JHN` and `DISPLAY_BONDS = True`.\n\nIf you change those variables and run the kernel, it will display 10 examples from small `sc_constant` to large `sc_constant` of the type desired. If you wish to display specific bonds of your choice, call the function `animate(j, title='', display_bonds=DISPLAY_BONDS)`. Set the variable `j = train.index[k]` for some bond number `k`.\n\nAfterward hydrogen is positioned at (0,0,0) and nitrogen (the other atom in coupling) is positioned at (1,0,0). Then the molecule is rotated around the x-axis. By viewing different molecules, you will notice that when coupling atoms connect to a ring of atoms, `sc_constant` is large and when they connect to a non-ring, `sc_constant` is small. Therefore detecting rings is helpful.\n\n![image](http://playagricola.com/Kaggle/b482119.gif)\n![image](http://playagricola.com/Kaggle/b582119.gif)\n\nSince this coupling is `2JHN` there is always 1 atom between the hydrogen and nitrogen. Most often it is carbon. But 1% of the time it is oxygen and 2% of the time it is another nitrogen. When it is oxygen, `sc_constant` is small because oxygen has 2 valence and won't make a ring. When it is another nitrogen it likes to make a ring and `sc_constant` is larger.\n![image](http://playagricola.com/Kaggle/pie82119.png)\n![image](http://playagricola.com/Kaggle/b382119.gif)\n![image](http://playagricola.com/Kaggle/b282119.gif)\n![image](http://playagricola.com/Kaggle/hist82119.png)\n\n[1]: https://www.kaggle.com/cdeotte/molecule-animations",
    "606031": "You are Amazing with Molecular Theory...!! @cdeotte"
  },
  "source": "meta"
}