{
  "id": 229258,
  "title": "Rdkit crashes when translate an InChI string I generated to molecule ",
  "url": "/competitions/bms-molecular-translation/discussion/229258",
  "author_name": "",
  "post_date": "2021-03-29T10:05:38.517872900Z",
  "votes": 5,
  "comment_count": 4,
  "views": 0,
  "content": "<p>from rdkit import Chem</p>\n<p>x='InChI=1S/C24H26O4/c1-24(2)19-13-17-15-7-5-4-6-14(15)8-10-20(17)27-22(18)18-12-16(23(25)26-3)9-11-21(18)28-23/h4-7,9,11-12,17,19-20,22H,8,10,13H2,1-3H3/t17-,19-,20-,22-/m0/s1'</p>\n<h1>rdkit crashes when translate x to molecule</h1>\n<p>Chem.MolFromInchi(x)</p>",
  "messages": [
    {
      "id": "1255881",
      "postDate": "03/29/2021 10:05:38",
      "content": "<p>from rdkit import Chem</p>\n<p>x='InChI=1S/C24H26O4/c1-24(2)19-13-17-15-7-5-4-6-14(15)8-10-20(17)27-22(18)18-12-16(23(25)26-3)9-11-21(18)28-23/h4-7,9,11-12,17,19-20,22H,8,10,13H2,1-3H3/t17-,19-,20-,22-/m0/s1'</p>\n<h1>rdkit crashes when translate x to molecule</h1>\n<p>Chem.MolFromInchi(x)</p>",
      "rawMarkdown": "from rdkit import Chem\n\nx='InChI=1S/C24H26O4/c1-24(2)19-13-17-15-7-5-4-6-14(15)8-10-20(17)27-22(18)18-12-16(23(25)26-3)9-11-21(18)28-23/h4-7,9,11-12,17,19-20,22H,8,10,13H2,1-3H3/t17-,19-,20-,22-/m0/s1'\n\n# rdkit crashes when translate x to molecule\nChem.MolFromInchi(x)",
      "votes": null
    },
    {
      "id": "1279390",
      "postDate": "04/20/2021 20:50:26",
      "content": "<p>I'm facing the same issue. It looks like this and crashes the kernel. <strong><code>try.. except...</code></strong> logic does not prevent this. I assume it's the segmentation fault problem that pops up in forums when discussion RDKit.</p>\n<pre><code>RDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: *Conversion failed on component(s) 1(C43H76N2O)\nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \n...\n...\n...\n</code></pre>",
      "rawMarkdown": "I'm facing the same issue. It looks like this and crashes the kernel. **`try.. except...`** logic does not prevent this. I assume it's the segmentation fault problem that pops up in forums when discussion RDKit.\n\n```\nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: *Conversion failed on component(s) 1(C43H76N2O)\nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \n...\n...\n...\n```",
      "votes": null
    },
    {
      "id": "1279393",
      "postDate": "04/20/2021 20:56:44",
      "content": "<p>See <a href=\"https://www.kaggle.com/wuliaokaola/bmsmt-0331-normalize-your-predictions\" target=\"_blank\">this kernel</a> for a way around this</p>",
      "rawMarkdown": "See [this kernel](https://www.kaggle.com/wuliaokaola/bmsmt-0331-normalize-your-predictions) for a way around this",
      "votes": null
    },
    {
      "id": "1325386",
      "postDate": "05/27/2021 17:50:36",
      "content": "<p>It seems that there is a problem already known by RDKit developers, but not solved yet. <code>try: ... except: ...</code> will not work as the program is not returning any exception or error message, just crashing due to a problem in their parser, or so they say. It seems bad handling of memory when you try to translate a molecule that does not exist or RDKit does not know.</p>",
      "rawMarkdown": "It seems that there is a problem already known by RDKit developers, but not solved yet. ```try: ... except: ...``` will not work as the program is not returning any exception or error message, just crashing due to a problem in their parser, or so they say. It seems bad handling of memory when you try to translate a molecule that does not exist or RDKit does not know.",
      "votes": null
    },
    {
      "id": "1325583",
      "postDate": "05/27/2021 20:55:12",
      "content": "<p>My workaround was to build a list of failing molecules and than just skip those - nothing else worked to try and trap the issue.  </p>",
      "rawMarkdown": "My workaround was to build a list of failing molecules and than just skip those - nothing else worked to try and trap the issue.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 1279390,
      "author_name": "dschettler8845",
      "author_url": "",
      "post_date": "04/20/2021 20:50:26",
      "content": "<p>I'm facing the same issue. It looks like this and crashes the kernel. <strong><code>try.. except...</code></strong> logic does not prevent this. I assume it's the segmentation fault problem that pops up in forums when discussion RDKit.</p>\n<pre><code>RDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: *Conversion failed on component(s) 1(C43H76N2O)\nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \n...\n...\n...\n</code></pre>",
      "votes": null,
      "replies": [
        {
          "id": 1279393,
          "author_name": "tuckerarrants",
          "author_url": "",
          "post_date": "04/20/2021 20:56:44",
          "content": "<p>See <a href=\"https://www.kaggle.com/wuliaokaola/bmsmt-0331-normalize-your-predictions\" target=\"_blank\">this kernel</a> for a way around this</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 1325386,
      "author_name": "fernando2393",
      "author_url": "",
      "post_date": "05/27/2021 17:50:36",
      "content": "<p>It seems that there is a problem already known by RDKit developers, but not solved yet. <code>try: ... except: ...</code> will not work as the program is not returning any exception or error message, just crashing due to a problem in their parser, or so they say. It seems bad handling of memory when you try to translate a molecule that does not exist or RDKit does not know.</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 1325583,
      "author_name": "pcjimmmy",
      "author_url": "",
      "post_date": "05/27/2021 20:55:12",
      "content": "<p>My workaround was to build a list of failing molecules and than just skip those - nothing else worked to try and trap the issue.  </p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "1255881": "from rdkit import Chem\n\nx='InChI=1S/C24H26O4/c1-24(2)19-13-17-15-7-5-4-6-14(15)8-10-20(17)27-22(18)18-12-16(23(25)26-3)9-11-21(18)28-23/h4-7,9,11-12,17,19-20,22H,8,10,13H2,1-3H3/t17-,19-,20-,22-/m0/s1'\n\n# rdkit crashes when translate x to molecule\nChem.MolFromInchi(x)",
    "1279390": "I'm facing the same issue. It looks like this and crashes the kernel. **`try.. except...`** logic does not prevent this. I assume it's the segmentation fault problem that pops up in forums when discussion RDKit.\n\n```\nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: *Conversion failed on component(s) 1(C43H76N2O)\nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \nRDKit ERROR: [20:47:34] ERROR: \n...\n...\n...\n```",
    "1279393": "See [this kernel](https://www.kaggle.com/wuliaokaola/bmsmt-0331-normalize-your-predictions) for a way around this",
    "1325386": "It seems that there is a problem already known by RDKit developers, but not solved yet. ```try: ... except: ...``` will not work as the program is not returning any exception or error message, just crashing due to a problem in their parser, or so they say. It seems bad handling of memory when you try to translate a molecule that does not exist or RDKit does not know.",
    "1325583": "My workaround was to build a list of failing molecules and than just skip those - nothing else worked to try and trap the issue."
  },
  "source": "meta"
}