Provides different representations for chemical compounds with a unique and defined chemical structure

Documentation, Representation, Examples

An OpenTox Compound resource is an instance of class ot:Compound, a subclass of ot:OpentoxResource.

  • Example 1. Retrieve compound as SMILES (Simplified Molecular Input Line Entry System)
     $ curl -H "Accept:chemical/x-daylight-smiles" https://apps.ideaconsult.net/ambit2/compound/1
     O=C
    
  • Example 2. Retrieve compound as SMILES, show HTTP headers
     $ curl -H "Accept:chemical/x-daylight-smiles" https://apps.ideaconsult.net/ambit2/compound/1 -i
     HTTP/1.1 200 OK
     Content-Type: chemical/x-daylight-smiles;charset=UTF-8
    
    O=C
    
  • Example 3. Retrieve compound as InChI
    $ curl -H "Accept:chemical/x-inchi" https://apps.ideaconsult.net/ambit2/compound/1
    InChI=1S/CH2O/c1-2/h1H2
    
  • Example 4. Retrieve compound in MOL format
    $ curl -H "Accept:chemical/x-mdl-molfile" https://apps.ideaconsult.net/ambit2/compound/1
    CH2O
    APtclcactv09040902283D 0   0.00000     0.00000
    
      4  3  0  0  0  0  0  0  0  0999 V2000
       -0.6004    0.0000    0.0001 O   0  0  0  0  0  0  0  0  0  0  0  0
        0.6072    0.0000   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0
        1.1472    0.9353    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
        1.1472   -0.9353    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
      1  2  2  0  0  0  0
      2  3  1  0  0  0  0
      2  4  1  0  0  0  0
    
  • Example 5. Retrieve compound in SDF format
    curl -H "Accept:chemical/x-mdl-sdfile" https://apps.ideaconsult.net/ambit2/compound/1
    CH2O
    APtclcactv09040902283D 0   0.00000     0.00000
    
      4  3  0  0  0  0  0  0  0  0999 V2000
       -0.6004    0.0000    0.0001 O   0  0  0  0  0  0  0  0  0  0  0  0
        0.6072    0.0000   -0.0004 C   0  0  0  0  0  0  0  0  0  0  0  0
        1.1472    0.9353    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
        1.1472   -0.9353    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
      1  2  2  0  0  0  0
      2  3  1  0  0  0  0
      2  4  1  0  0  0  0
    M  END
    $$$$
    
  • Example 6. Retrieve compound in CML format
    $ curl -H "Accept:chemical/x-cml" https://apps.ideaconsult.net/ambit2/compound/1
    <?xml version="1.0" encoding="ISO-8859-1"?><list dictRef="cdk:moleculeSet" xmlns="http://www.xml-cml.org/schema">
    <molecule id="m1" title="CH2O" xmlns="http://www.xml-cml.org/schema">
      <atomArray>
        <atom id="a1" elementType="O" x3="-0.6004" y3="0.0" z3="1.0E-4" formalCharge="0" isotopeNumber="16"/>
        <atom id="a2" elementType="C" x3="0.6072" y3="0.0" z3="-4.0E-4" formalCharge="0" isotopeNumber="12"/>
        <atom id="a3" elementType="H" x3="1.1472" y3="0.9353" z3="0.0016" formalCharge="0" isotopeNumber="1"/>
        <atom id="a4" elementType="H" x3="1.1472" y3="-0.9353" z3="0.0016" formalCharge="0" isotopeNumber="1"/>
      </atomArray>
      <bondArray>
        <bond id="b1" atomRefs2="a1 a2" order="D"/>
        <bond id="b2" atomRefs2="a2 a3" order="S"/>
        <bond id="b3" atomRefs2="a2 a4" order="S"/>
      </bondArray>
      <scalar dictRef="cdk:molecularProperty" title="cdk:Remark" dataType="xsd:string"/>
    </molecule>
    </list>
    

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Last Published: 2017-09-27.