The AMBIT Project

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

http://opentox.org/dev/apis/api-1.2/structure

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>

OpenTox API : Compound