{
  "id": 225130,
  "title": "Understanding each layer of InChI, the numbering order of atoms",
  "url": "/competitions/bms-molecular-translation/discussion/225130",
  "author_name": "codistry",
  "post_date": "2021-03-11T00:29:51.703000",
  "votes": 7,
  "comment_count": 0,
  "views": 0,
  "content": "<p>Here is a thought on how to simplify InChI. Instead of figuring out each layer independently in InChI while worrying about consistency between layers, there is only a few key information that are needed to derive and generate all layers.</p>\n<p>The most important information is the skeleton information, including:<br>\n1) How many lines, and what type of lines (single, double, wavy, dot) in the picture<br>\n2) How many comers in the picture, and the connections between corners<br>\n3) What letters other than “H” in the picture<br>\n4) Give each corner and loose end of lines (meaning atoms except for H) a number starting from 1 and Carbon. There is a complicated rule for how each atom is assigned a number sequentially. See more details at the end.</p>\n<p>Given the above questions answered, the InChI can be generated:<br>\n<strong>Starting layer:</strong> InChI = 1S<br>\n<strong>Skeleton connection layer:</strong> find the longest skeleton connection, and add additional connection using ()<br>\n<strong>Hydrogen layer:</strong> count the no. of connections of each atom<br>\nthe No. of H for carbon = 4 - no. of connections <br>\nthe No. of H for oxygen= 2 - no. of connections <br>\n<strong>Formula layer:</strong> list each atom identified followed by the no. of occurrence<br>\n<strong>Stereochemistry layer:</strong> add this layer when dot/wavy line identified (see <a href=\"https://en.wikipedia.org/wiki/Enantiomer\" target=\"_blank\">https://en.wikipedia.org/wiki/Enantiomer</a> )</p>\n<p><strong>How the sequential order is assigned to each atom.</strong><br>\nThe basic rule is carbon, others in alphabetic. Then by the number of connections on each atom from least to most. <br>\nThe detailed explanation can be found here:<br>\n<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486400/\" target=\"_blank\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486400/</a></p>",
  "messages": [
    {
      "id": 1234112,
      "postDate": "2021-03-11T00:29:51.703Z",
      "content": "<p>Here is a thought on how to simplify InChI. Instead of figuring out each layer independently in InChI while worrying about consistency between layers, there is only a few key information that are needed to derive and generate all layers.</p>\n<p>The most important information is the skeleton information, including:<br>\n1) How many lines, and what type of lines (single, double, wavy, dot) in the picture<br>\n2) How many comers in the picture, and the connections between corners<br>\n3) What letters other than “H” in the picture<br>\n4) Give each corner and loose end of lines (meaning atoms except for H) a number starting from 1 and Carbon. There is a complicated rule for how each atom is assigned a number sequentially. See more details at the end.</p>\n<p>Given the above questions answered, the InChI can be generated:<br>\n<strong>Starting layer:</strong> InChI = 1S<br>\n<strong>Skeleton connection layer:</strong> find the longest skeleton connection, and add additional connection using ()<br>\n<strong>Hydrogen layer:</strong> count the no. of connections of each atom<br>\nthe No. of H for carbon = 4 - no. of connections <br>\nthe No. of H for oxygen= 2 - no. of connections <br>\n<strong>Formula layer:</strong> list each atom identified followed by the no. of occurrence<br>\n<strong>Stereochemistry layer:</strong> add this layer when dot/wavy line identified (see <a href=\"https://en.wikipedia.org/wiki/Enantiomer\" target=\"_blank\">https://en.wikipedia.org/wiki/Enantiomer</a> )</p>\n<p><strong>How the sequential order is assigned to each atom.</strong><br>\nThe basic rule is carbon, others in alphabetic. Then by the number of connections on each atom from least to most. <br>\nThe detailed explanation can be found here:<br>\n<a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486400/\" target=\"_blank\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486400/</a></p>",
      "rawMarkdown": "Here is a thought on how to simplify InChI. Instead of figuring out each layer independently in InChI while worrying about consistency between layers, there is only a few key information that are needed to derive and generate all layers.\n\nThe most important information is the skeleton information, including:\n1) How many lines, and what type of lines (single, double, wavy, dot) in the picture\n2) How many comers in the picture, and the connections between corners\n3) What letters other than “H” in the picture\n4) Give each corner and loose end of lines (meaning atoms except for H) a number starting from 1 and Carbon. There is a complicated rule for how each atom is assigned a number sequentially. See more details at the end.\n\nGiven the above questions answered, the InChI can be generated:\n**Starting layer:** InChI = 1S\n**Skeleton connection layer:** find the longest skeleton connection, and add additional connection using ()\n**Hydrogen layer:** count the no. of connections of each atom\nthe No. of H for carbon = 4 - no. of connections \nthe No. of H for oxygen= 2 - no. of connections \n**Formula layer:** list each atom identified followed by the no. of occurrence\n**Stereochemistry layer:** add this layer when dot/wavy line identified (see https://en.wikipedia.org/wiki/Enantiomer )\n\n**How the sequential order is assigned to each atom.**\nThe basic rule is carbon, others in alphabetic. Then by the number of connections on each atom from least to most. \nThe detailed explanation can be found here:\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486400/\n",
      "votes": 7
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "1234112": "Here is a thought on how to simplify InChI. Instead of figuring out each layer independently in InChI while worrying about consistency between layers, there is only a few key information that are needed to derive and generate all layers.\n\nThe most important information is the skeleton information, including:\n1) How many lines, and what type of lines (single, double, wavy, dot) in the picture\n2) How many comers in the picture, and the connections between corners\n3) What letters other than “H” in the picture\n4) Give each corner and loose end of lines (meaning atoms except for H) a number starting from 1 and Carbon. There is a complicated rule for how each atom is assigned a number sequentially. See more details at the end.\n\nGiven the above questions answered, the InChI can be generated:\n**Starting layer:** InChI = 1S\n**Skeleton connection layer:** find the longest skeleton connection, and add additional connection using ()\n**Hydrogen layer:** count the no. of connections of each atom\nthe No. of H for carbon = 4 - no. of connections \nthe No. of H for oxygen= 2 - no. of connections \n**Formula layer:** list each atom identified followed by the no. of occurrence\n**Stereochemistry layer:** add this layer when dot/wavy line identified (see https://en.wikipedia.org/wiki/Enantiomer )\n\n**How the sequential order is assigned to each atom.**\nThe basic rule is carbon, others in alphabetic. Then by the number of connections on each atom from least to most. \nThe detailed explanation can be found here:\nhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486400/\n"
  }
}