{
  "id": 566792,
  "title": "typo error in computation of tm score in overview page",
  "url": "/competitions/stanford-rna-3d-folding/discussion/566792",
  "author_name": "",
  "post_date": "2025-03-06T21:16:36.693934600Z",
  "votes": 3,
  "comment_count": 2,
  "views": 0,
  "content": "<p>there is a typo error in overview page:</p>\n<pre><code> Lref ≥ ; and d0 = ., ., ., ., or . for Lref &lt;, -, -, -, or -, respectively.\n</code></pre>\n<p>it should have been</p>\n<pre><code>  &lt;, -, ...\n</code></pre>",
  "messages": [
    {
      "id": "3143028",
      "postDate": "03/06/2025 21:16:36",
      "content": "<p>there is a typo error in overview page:</p>\n<pre><code> Lref ≥ ; and d0 = ., ., ., ., or . for Lref &lt;, -, -, -, or -, respectively.\n</code></pre>\n<p>it should have been</p>\n<pre><code>  &lt;, -, ...\n</code></pre>",
      "rawMarkdown": "there is a typo error in overview page:\n\n```\nfor Lref ≥ 30; and d0 = 0.3, 0.4, 0.5, 0.6, or 0.7 for Lref <15, 12-15, 16-19, 20-23, or 24-29, respectively.\n\n```\n\nit should have been\n\n```\n Lref <12, 12-15, ...\n\n```",
      "votes": null
    },
    {
      "id": "3143060",
      "postDate": "03/06/2025 22:37:05",
      "content": "<p>Thanks for pointing it out. Fixed!</p>",
      "rawMarkdown": "Thanks for pointing it out. Fixed!",
      "votes": null
    },
    {
      "id": "3143633",
      "postDate": "03/07/2025 12:23:29",
      "content": "<p>for those who want to make python code for the kaggle metric, please note:<br>\nthe orginal usalign.cpp</p>\n<pre><code> standard_TMscore( **r1,  **r2,  **xtm,  **ytm,\n     **xt,  **x,  **y,  xlen,  ylen,  invmap[],\n    &amp; L_ali, &amp; RMSD,  D0_MIN,  Lnorm,  d0,\n     d0_search,  score_d8,  t[],  u[][],\n      mol_type)\n{\n    D0_MIN = ;\n    Lnorm = ylen;\n     (mol_type&gt;) \n    {\n             (Lnorm&lt;=) d0=; \n         (Lnorm&gt; &amp;&amp; Lnorm&lt;=) d0=;\n         (Lnorm&gt; &amp;&amp; Lnorm&lt;=) d0=;\n         (Lnorm&gt; &amp;&amp; Lnorm&lt;=) d0=;\n         (Lnorm&gt; &amp;&amp; Lnorm&lt;)  d0=;\n         d0=(*pow((Lnorm*), /));\n    }\n    \n    {\n         (Lnorm &gt; ) d0=(*pow((Lnorm*), /) );\n         d0 = D0_MIN;\n         (d0 &lt; D0_MIN) d0 = D0_MIN;\n    }\n     d0_input = d0;\n</code></pre>",
      "rawMarkdown": "for those who want to make python code for the kaggle metric, please note:\nthe orginal usalign.cpp\n\n```\n\n\ndouble standard_TMscore(double **r1, double **r2, double **xtm, double **ytm,\n    double **xt, double **x, double **y, int xlen, int ylen, int invmap[],\n    int& L_ali, double& RMSD, double D0_MIN, double Lnorm, double d0,\n    double d0_search, double score_d8, double t[3], double u[3][3],\n    const int mol_type)\n{\n    D0_MIN = 0.5;\n    Lnorm = ylen;\n    if (mol_type>0) // RNA\n    {\n        if     (Lnorm<=11) d0=0.3; \n        else if(Lnorm>11 && Lnorm<=15) d0=0.4;\n        else if(Lnorm>15 && Lnorm<=19) d0=0.5;\n        else if(Lnorm>19 && Lnorm<=23) d0=0.6;\n        else if(Lnorm>23 && Lnorm<30)  d0=0.7;\n        else d0=(0.6*pow((Lnorm*1.0-0.5), 1.0/2)-2.5);\n    }\n    else\n    {\n        if (Lnorm > 21) d0=(1.24*pow((Lnorm*1.0-15), 1.0/3) -1.8);\n        else d0 = D0_MIN;\n        if (d0 < D0_MIN) d0 = D0_MIN;\n    }\n    double d0_input = d0;// Scaled by seq_min\n\n\n```",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3143060,
      "author_name": "inversion",
      "author_url": "",
      "post_date": "03/06/2025 22:37:05",
      "content": "<p>Thanks for pointing it out. Fixed!</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 3143633,
      "author_name": "hengck23",
      "author_url": "",
      "post_date": "03/07/2025 12:23:29",
      "content": "<p>for those who want to make python code for the kaggle metric, please note:<br>\nthe orginal usalign.cpp</p>\n<pre><code> standard_TMscore( **r1,  **r2,  **xtm,  **ytm,\n     **xt,  **x,  **y,  xlen,  ylen,  invmap[],\n    &amp; L_ali, &amp; RMSD,  D0_MIN,  Lnorm,  d0,\n     d0_search,  score_d8,  t[],  u[][],\n      mol_type)\n{\n    D0_MIN = ;\n    Lnorm = ylen;\n     (mol_type&gt;) \n    {\n             (Lnorm&lt;=) d0=; \n         (Lnorm&gt; &amp;&amp; Lnorm&lt;=) d0=;\n         (Lnorm&gt; &amp;&amp; Lnorm&lt;=) d0=;\n         (Lnorm&gt; &amp;&amp; Lnorm&lt;=) d0=;\n         (Lnorm&gt; &amp;&amp; Lnorm&lt;)  d0=;\n         d0=(*pow((Lnorm*), /));\n    }\n    \n    {\n         (Lnorm &gt; ) d0=(*pow((Lnorm*), /) );\n         d0 = D0_MIN;\n         (d0 &lt; D0_MIN) d0 = D0_MIN;\n    }\n     d0_input = d0;\n</code></pre>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3143028": "there is a typo error in overview page:\n\n```\nfor Lref ≥ 30; and d0 = 0.3, 0.4, 0.5, 0.6, or 0.7 for Lref <15, 12-15, 16-19, 20-23, or 24-29, respectively.\n\n```\n\nit should have been\n\n```\n Lref <12, 12-15, ...\n\n```",
    "3143060": "Thanks for pointing it out. Fixed!",
    "3143633": "for those who want to make python code for the kaggle metric, please note:\nthe orginal usalign.cpp\n\n```\n\n\ndouble standard_TMscore(double **r1, double **r2, double **xtm, double **ytm,\n    double **xt, double **x, double **y, int xlen, int ylen, int invmap[],\n    int& L_ali, double& RMSD, double D0_MIN, double Lnorm, double d0,\n    double d0_search, double score_d8, double t[3], double u[3][3],\n    const int mol_type)\n{\n    D0_MIN = 0.5;\n    Lnorm = ylen;\n    if (mol_type>0) // RNA\n    {\n        if     (Lnorm<=11) d0=0.3; \n        else if(Lnorm>11 && Lnorm<=15) d0=0.4;\n        else if(Lnorm>15 && Lnorm<=19) d0=0.5;\n        else if(Lnorm>19 && Lnorm<=23) d0=0.6;\n        else if(Lnorm>23 && Lnorm<30)  d0=0.7;\n        else d0=(0.6*pow((Lnorm*1.0-0.5), 1.0/2)-2.5);\n    }\n    else\n    {\n        if (Lnorm > 21) d0=(1.24*pow((Lnorm*1.0-15), 1.0/3) -1.8);\n        else d0 = D0_MIN;\n        if (d0 < D0_MIN) d0 = D0_MIN;\n    }\n    double d0_input = d0;// Scaled by seq_min\n\n\n```"
  },
  "source": "meta"
}