Metamolecular Products Blog

Chemcaster now supports exact structure queries, both through the graphical administrative interface and through the Web API.

The new capability can be tested using the curl HTTP client. As an example, prepare a file called query.xml in your working directory with this content - representing an exact structure search for benzene:

<?xml version="1.0" encoding="UTF-8"?>
<query>
  <molfile>[NO NAME]
  CHEMWRIT          2D
Created with ChemWriter - http://metamolecular.com/chemwriter
  6  6  0  0  0  0  0  0  0  0  0 V2000
   -1.2400    1.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3740    0.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    1.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    2.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3740    2.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    2.0200    0.0000 C   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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
M  END</molfile>
</query>

We can now issue a POST request, assuming a registry id of 1, to create a new query:

$ curl -H 'Accept: application/xml' -H 'Content-Type: application/xml' -F upload=@query.xml -u you@example.com:password https://chemcaster.com/registries/1/queries

This responds with the following xml and a code of 201 (Created):

<?xml version="1.0" encoding="UTF-8"?>
<query>
  <id type="integer">2</id>
  <molfile>[NO NAME]
  CHEMWRIT          2D
Created with ChemWriter - http://metamolecular.com/chemwriter
  6  6  0  0  0  0  0  0  0  0  0 V2000
   -1.2400    1.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3740    0.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    1.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    2.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3740    2.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    2.0200    0.0000 C   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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
M  END</molfile>
</query>

We can read the Query ID ('2') and then retrieve our search results with:

$ curl -H 'Accept: application/xml' -u you@example.com:secret https://chemcaster.com/queries/2

The response contains the original query in molfile format as well as the name and id of the matching structure:

<query>
  <id type="integer">2</id>
  <registry-id type="integer">1</registry-id>
  <molfile>[NO NAME]
  CHEMWRIT          2D
Created with ChemWriter - http://metamolecular.com/chemwriter
  6  6  0  0  0  0  0  0  0  0  0 V2000
   -1.2400    1.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3740    0.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    1.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4921    2.0200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3740    2.5200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400    2.0200    0.0000 C   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
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
M  END</molfile>
  <results type="array">
    <structure>
      <id>16</id>
      <name>benzene</name>
    </structure>
  </results>
</query>

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