Skip to content

VRmol API Services

Jump to bottom
Kui Xu edited this page May 30, 2020 · 1 revision

VRmol API Services

You can access VRmol API Services (including drug drug docking, genomic variations, speech recognition, sequence conservation visualization) by URL. Option settings are listed below. Once you request the service, VRmol will response and return with a json format string, which consists of data or warning information.

Genomic Variations

Options Data Type Value Comment
taskid Integer 10 Request Genomic Variations for the provided structure
pdbid String PDB code 4 charactors
ds String TCGA, CCLE, EXAC Genomic Variations Database Name
Example 1:
https://vrmol.net/server/api.php?taskid=10&pdbid=1MBD&ds=tcga 
{
  "code": 0,
  "message": "no corresponding Uniprot-AC"
}

Example 2: https://vrmol.net/server/api.php?taskid=10&pdbid=2YGD&ds=ccle

{
  "code": 0,
  "message": "no mutation information in the current CCLE database."
}

Example 3: https://vrmol.net/server/api.php?taskid=10&pdbid=2YGD&ds=tcga

{
  "code": 1,
  "data": {
    "mutations": [
      {
        "id": "832951",
        "v_class": "Missense_Mutation",
        "v_type": "SNP",
        "g_change": "g.chr11:111779667C>G",
        "p_change": "p.E117Q",
        "disease": "UCEC",
        "pos": "117"
      },
      {
        "id": "832952",
        "v_class": "Missense_Mutation",
        "v_type": "SNP",
        "g_change": "g.chr11:111781056G>A",
        "p_change": "p.R107C",
        "disease": "UCEC",
        "pos": "107"
      },
      {
        "id": "832953",
        "v_class": "Silent",
        "v_type": "SNP",
        "g_change": "g.chr11:111781108G>T",
        "p_change": "p.L89L",
        "disease": "UCEC",
        "pos": "89"
      },
      {
        "id": "79882",
        "v_class": "Silent",
        "v_type": "SNP",
        "g_change": "g.chr11:111779560G>A",
        "p_change": "p.V152V",
        "disease": "SKCM",
        "pos": "152"
      },
      {
        "id": "118368",
        "v_class": "Missense_Mutation",
        "v_type": "SNP",
        "g_change": "g.chr11:111782377A>C",
        "p_change": "p.F24L",
        "disease": "SKCM",
        "pos": "24"
      },
      {
        "id": "390477",
        "v_class": "Silent",
        "v_type": "SNP",
        "g_change": "g.chr11:111782347C>T",
        "p_change": "p.E34E",
        "disease": "STAD",
        "pos": "34"
      },
      {
        "id": "646695",
        "v_class": "Missense_Mutation",
        "v_type": "SNP",
        "g_change": "g.chr11:111779603G>A",
        "p_change": "p.S138L",
        "disease": "LUAD",
        "pos": "138"
      }
    ],
    "chains": [
      "A",
      "B",
      "C",
      "D",
      "E",
      "F",
      "G",
      "H",
      "I",
      "J",
      "K",
      "L",
      "M",
      "N",
      "O",
      "P",
      "Q",
      "R",
      "S",
      "T",
      "U",
      "V",
      "W",
      "X"
    ],
    "pdbid": "2YGD",
    "dataset": "tcga"
  },
  "message": "success"
}

Sequence Conservation

Options Data Type Value Comment
taskid Integer 11 Request Sequence Conservation for the provided structure
pdbid String PDB code 4 charactors
chain String TCGA, CCLE, EXAC Chain Name
Example 1:
https://vrmol.net/server/api.php?taskid=11&pdbid=3IVD&chain=A 
{
    code: 1,
    datas: [
    {
        pos: "1",
        seq: "M",
        resname: "",
        resid: "",
        chain: "",
        score: "0.013",
        color: "5",
        confinter: "-0.705,0.469",
        confintercolor: "7,4",
        msa: "8/301",
        resvar: "F,M,D,L"
    },
    {
        pos: "2",
        seq: "S",
        resname: "",
        resid: "",
        chain: "",
        score: "0.253",
        color: "4",
        confinter: "-0.355,0.687",
        confintercolor: "6,3",
        msa: "20/301",
        resvar: "A,S,T,D,K,G"
    },
...

Drug data API

Options Data Type Value Comment
taskid Integer 12 Request Related drugs for the provided structure
pdbid String PDB code 4 charactors
Example:
http://vrmol.net/server/api.php?taskid=12&pdbid=2BR9 
{
    code: 1,
    data: [
        {
            id: "77",
            uniprotac: "P62258",
            bindingdb: "",
            chembl: "CHEMBL3329082;",
            swisslipids: "",
            guidetopharmacology: "",
            drugbank: "DB01780;"
        }
    ],
    message: "success"
}

EMDB

Options Data Type Value Comment
taskid Integer 13 Request related electronic density map for the provided structure
pdbid String PDB code 4 charactors

Example: https://vrmol.net/server/api.php?taskid=13&pdbid=1MI6

{
   code: 1,
   data: [
       "1006",
       "1007",
       "1008",
       "1009",
       "1010"
   ],
   message: "success"
}

Drug Docking

Options Data Type Value Comment
taskid Integer 10 Access AutoDock service
pdbid String PDB code 4 charactors
smolid String drug name in DrugBank drug name
x_c Float * x value of center position of the docking area
y_c Float * y value of center of the docking area
z_c Float * z value of center of the docking area
x_s Float * width value of the docking area
y_s Float * height value of the docking area
z_s Float * length value of the docking area
Example:
https://vrmol.net/server/autodock/autodock.php?pdbid=1mbs&smolid=DB04464&x_c=10&y_c=10&z_c=10&x_s=50&y_s=50&z_s=50 
{
   jobid : "1mbs_DB04464_20181223200624_92",
   log : "http:\/\/vr.zhanglab.net\/server\/autodock\/jobs\/1mbs_DB04464_20181223200624_92\/log",
   pdbid : "1mbs",
   smolid : "DB04464",
   fullmodel : "DB04464_out.pdb",
   fullmodel_url : "http:\/\/vr.zhanglab.net\/server\/autodock\/jobs\/1mbs_DB04464_20181223200624_92\/DB04464_out.pdb",
   model_list":       ["DB04464_out_1.pdb","DB04464_out_2.pdb","DB04464_out_3.pdb","DB04464_out_4.pdb","DB04464_out_5.pdb","DB04464_out_6.pdb","DB04464_out_7.pdb","DB04464_out_8.pdb","DB04464_out_9.pdb"],
   outdir : "http:\/\/vr.zhanglab.net\/server\/autodock\/jobs\/1mbs_DB04464_20181223200624_92"
}

Speech Recognition

For accessing Speech Recognition service, you only need to import https://vrmol.net/server/listen/recorder.js into your html code.

Example:

<html>
    <meta http-equiv="Content-Type"content="text/html; charset=utf-8"/>
    <script src="jquery-3.2.1.min.js"></script>
    <script src="https://vrmol.net/server/listen/recorder.js"></script>
    <body>
        <div class="messages"></div>
        <button class="test" onmousedown="startRecording()" onmouseup="endRecording()">Voice</button>
        <br>
        <input name="language" value="Chinese" type="radio" id="Chinese" onclick="getlanguage()" checked="true">
        <label for="Chinese">For Chinese</label>
        <br>
        <input name="language" value="English" type="radio" id="English" onclick="getlanguage()">
        <label for="English">For English</label>
        <br>
    </body>
</html>
Clone this wiki locally