{
  "id": 96777,
  "title": "X, Y and Z coordinates and atom index",
  "url": "/competitions/champs-scalar-coupling/discussion/96777",
  "author_name": "",
  "post_date": "2019-06-23T00:53:10.481290300Z",
  "votes": 3,
  "comment_count": 6,
  "views": 0,
  "content": "<p>The data description says:</p>\n\n<blockquote>\n  <p>the remaining columns contain the X, Y and Z cartesian coordinates (a standard format for chemists and molecular visualization programs)</p>\n</blockquote>\n\n<p>I was wondering if someone could give me more information on the exact meaning of these coordinates. Does the exact position of an atom matter or just the relative position to the rest of the atoms in the molecule matter? <strong>In other words, if I rotate certain degrees a molecule is still the same molecule?</strong> I would say that it is the same, but I don't know, maybe they are oriented that way because the generated magnetic field of the spins disposes them that way. I have totally made up that last sentence, I am a great ignorant in the world of chemistry ^.^</p>\n\n<p>I have a similar question related to the atom index. <strong>Saying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?</strong>\nWhy does an atom have the id 0? Does it have any meaning or is it only a meaningless assigned ID?</p>\n\n<p>Both coordinates and index seem to be important for the first predictive models I'm building, that confuses me a little... Thanks for your help!!</p>",
  "messages": [
    {
      "id": "558805",
      "postDate": "06/23/2019 00:53:10",
      "content": "<p>The data description says:</p>\n\n<blockquote>\n  <p>the remaining columns contain the X, Y and Z cartesian coordinates (a standard format for chemists and molecular visualization programs)</p>\n</blockquote>\n\n<p>I was wondering if someone could give me more information on the exact meaning of these coordinates. Does the exact position of an atom matter or just the relative position to the rest of the atoms in the molecule matter? <strong>In other words, if I rotate certain degrees a molecule is still the same molecule?</strong> I would say that it is the same, but I don't know, maybe they are oriented that way because the generated magnetic field of the spins disposes them that way. I have totally made up that last sentence, I am a great ignorant in the world of chemistry ^.^</p>\n\n<p>I have a similar question related to the atom index. <strong>Saying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?</strong>\nWhy does an atom have the id 0? Does it have any meaning or is it only a meaningless assigned ID?</p>\n\n<p>Both coordinates and index seem to be important for the first predictive models I'm building, that confuses me a little... Thanks for your help!!</p>",
      "rawMarkdown": "The data description says:\n&gt; the remaining columns contain the X, Y and Z cartesian coordinates (a standard format for chemists and molecular visualization programs)\n\nI was wondering if someone could give me more information on the exact meaning of these coordinates. Does the exact position of an atom matter or just the relative position to the rest of the atoms in the molecule matter? **In other words, if I rotate certain degrees a molecule is still the same molecule?** I would say that it is the same, but I don't know, maybe they are oriented that way because the generated magnetic field of the spins disposes them that way. I have totally made up that last sentence, I am a great ignorant in the world of chemistry ^.^\n\nI have a similar question related to the atom index. **Saying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?**\nWhy does an atom have the id 0? Does it have any meaning or is it only a meaningless assigned ID?\n\nBoth coordinates and index seem to be important for the first predictive models I'm building, that confuses me a little... Thanks for your help!!",
      "votes": null
    },
    {
      "id": "558811",
      "postDate": "06/23/2019 01:21:13",
      "content": "<p>For your first question, only the relative position of the atoms matters.  If the atom is rotated, the X, Y, Z coordinates will change.  However, they will all change relative to each other.  For your second question, there is probably a chemistry standard for assigning the index numbers.  I personally don't use either of these features in my model.</p>",
      "rawMarkdown": "For your first question, only the relative position of the atoms matters.  If the atom is rotated, the X, Y, Z coordinates will change.  However, they will all change relative to each other.  For your second question, there is probably a chemistry standard for assigning the index numbers.  I personally don't use either of these features in my model.",
      "votes": null
    },
    {
      "id": "559007",
      "postDate": "06/23/2019 10:38:25",
      "content": "<p>Thank you, very useful information to start looking for new features!</p>",
      "rawMarkdown": "Thank you, very useful information to start looking for new features!",
      "votes": null
    },
    {
      "id": "561429",
      "postDate": "06/26/2019 12:52:01",
      "content": "<p>The id is meaningless and is just to keep track of the atoms. You could change the order of any atom in a molecule and get the same physical observables, as long as you update the indices accordingly.</p>",
      "rawMarkdown": "The id is meaningless and is just to keep track of the atoms. You could change the order of any atom in a molecule and get the same physical observables, as long as you update the indices accordingly.",
      "votes": null
    },
    {
      "id": "562513",
      "postDate": "06/27/2019 10:12:01",
      "content": "<p>About your question below,\nSaying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?\nThe answer is yes, it is true. The conection between them and also the type of bond must be the same.</p>",
      "rawMarkdown": "About your question below,\nSaying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?\nThe answer is yes, it is true. The conection between them and also the type of bond must be the same.",
      "votes": null
    },
    {
      "id": "562838",
      "postDate": "06/27/2019 15:27:19",
      "content": "<p>Thank you Lars!</p>",
      "rawMarkdown": "Thank you Lars!",
      "votes": null
    },
    {
      "id": "562841",
      "postDate": "06/27/2019 15:29:12",
      "content": "<p>Thank you! I am no longer using xyz coordinates or atomic indices in my models.</p>",
      "rawMarkdown": "Thank you! I am no longer using xyz coordinates or atomic indices in my models.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 558811,
      "author_name": "petersk20",
      "author_url": "",
      "post_date": "06/23/2019 01:21:13",
      "content": "<p>For your first question, only the relative position of the atoms matters.  If the atom is rotated, the X, Y, Z coordinates will change.  However, they will all change relative to each other.  For your second question, there is probably a chemistry standard for assigning the index numbers.  I personally don't use either of these features in my model.</p>",
      "votes": null,
      "replies": [
        {
          "id": 559007,
          "author_name": "guiferviz",
          "author_url": "",
          "post_date": "06/23/2019 10:38:25",
          "content": "<p>Thank you, very useful information to start looking for new features!</p>",
          "votes": null,
          "replies": []
        },
        {
          "id": 561429,
          "author_name": "larsbratholm",
          "author_url": "",
          "post_date": "06/26/2019 12:52:01",
          "content": "<p>The id is meaningless and is just to keep track of the atoms. You could change the order of any atom in a molecule and get the same physical observables, as long as you update the indices accordingly.</p>",
          "votes": null,
          "replies": []
        },
        {
          "id": 562838,
          "author_name": "guiferviz",
          "author_url": "",
          "post_date": "06/27/2019 15:27:19",
          "content": "<p>Thank you Lars!</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 562513,
      "author_name": "gtteixeira",
      "author_url": "",
      "post_date": "06/27/2019 10:12:01",
      "content": "<p>About your question below,\nSaying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?\nThe answer is yes, it is true. The conection between them and also the type of bond must be the same.</p>",
      "votes": null,
      "replies": [
        {
          "id": 562841,
          "author_name": "guiferviz",
          "author_url": "",
          "post_date": "06/27/2019 15:29:12",
          "content": "<p>Thank you! I am no longer using xyz coordinates or atomic indices in my models.</p>",
          "votes": null,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "558805": "The data description says:\n&gt; the remaining columns contain the X, Y and Z cartesian coordinates (a standard format for chemists and molecular visualization programs)\n\nI was wondering if someone could give me more information on the exact meaning of these coordinates. Does the exact position of an atom matter or just the relative position to the rest of the atoms in the molecule matter? **In other words, if I rotate certain degrees a molecule is still the same molecule?** I would say that it is the same, but I don't know, maybe they are oriented that way because the generated magnetic field of the spins disposes them that way. I have totally made up that last sentence, I am a great ignorant in the world of chemistry ^.^\n\nI have a similar question related to the atom index. **Saying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?**\nWhy does an atom have the id 0? Does it have any meaning or is it only a meaningless assigned ID?\n\nBoth coordinates and index seem to be important for the first predictive models I'm building, that confuses me a little... Thanks for your help!!",
    "558811": "For your first question, only the relative position of the atoms matters.  If the atom is rotated, the X, Y, Z coordinates will change.  However, they will all change relative to each other.  For your second question, there is probably a chemistry standard for assigning the index numbers.  I personally don't use either of these features in my model.",
    "559007": "Thank you, very useful information to start looking for new features!",
    "561429": "The id is meaningless and is just to keep track of the atoms. You could change the order of any atom in a molecule and get the same physical observables, as long as you update the indices accordingly.",
    "562513": "About your question below,\nSaying that atom 0 and atom 1 are connected is the same as saying that atom 1 and atom 0 are connected?\nThe answer is yes, it is true. The conection between them and also the type of bond must be the same.",
    "562838": "Thank you Lars!",
    "562841": "Thank you! I am no longer using xyz coordinates or atomic indices in my models."
  },
  "source": "meta"
}