Unable to create JPEG from Marin Applet using web services

Hi, I'm trying to use the WebService method batchConvert to convert the chemical structure in the Marin applet to a jpeg. I have tried to use the mrv and the mol format.

We are storing the mrv structure in the database because the structure and contents needs to be retrieved as they are added to the applet.

 

Can you please explain which webservice method and what input I should use to convert this mrv structure to an jpeg image.

 

I have tried several attempts as can be seen in the attached word document,

Is there a working example that I could reference?

Kind Regards

Karl

Karl,

We are trying to reproduce your error. 

The image output (e.g. jpeg output) is returned in base64 output. 

 

Jon

Karl,

You may want to ensure that the molecule structure does not interfere with the SOAP message structure.

<batchConvert
xmlns="http://webservice.jchem.chemaxon"><batchTarget>

<cml>

<MDocument>

 
<MChemicalStruct>

    <molecule molID="m1">

For example, this is a batchStandardize example received directly from the server.  Note the "<" are converted to "&lt;" before sending over html.  The newlines are converted to "&#xd;", although It might not be entirely necessary. 

<ns1:batchStandardize>
      <ns1:targetStructure>
        &lt;?xml version="1.0" ?>
        &#xd;
        &lt;cml>
        &#xd;
        &lt;MDocument>
        &#xd;
          &lt;MChemicalStruct>
        &#xd;
            &lt;molecule title="C6H11NO5" molID="m1">

Also note that SDF will also have problems generally with the "<" in the extended information section.

>  <UNIQUE_SMILES>
NC[C@@H]1CCCN1

 

To help debug, it would be useful to setup the Soap Monitor on the web server to get the exact messages that are being sent. Follow the link below for setup instructions and send us an example message. 

https://www.chemaxon.com/webservices/FAQ.html#soapmonitor

Please find attached a word document which has the output from the SOAPMonitor,

 

If further information is required, please feel free to ask,

 

Karl

Just a quick update,

I got the web service call to create an image from a smiles structure as can be seen in the attached screen shot. Just to see if there was a problem with the soap messaging, and it works perfectly.

So the soap messaging communication is ok, but it still wont work for the mrv structure. When I decode the xml response for the mrv stucture I'm getting a blank image.

 

I hope this helps and speeds up you finding a resolution to this issue,

 

Kind Regards

Karl

 

Karl,

Thanks for the information you have provided.

We have reproduced the problem and investigating solutions and workarounds.

 

Jon

Karl,

We have implemented a solution which will be included in an upcoming release.  This should be JChem 5.3.5.

 

As a work around, you can convert the mrv file into sdf file and then convert into jpeg. Please remember to escape the appropriate characters (e.g. < and >) when sending over http.  Also, all binary output like images will be base64 encoded.

 

Jon

Hi, when do you foresee Chem 5.3.5 being release?

 

Thanks

Karl

Karl,

5.3.5 will probably be released in July.

 

Jon

Karl,

The version will be in the July Release (probably called 5.3.6).

Jon

Hi Karl,

JChem 5.3.6 has been released with a fix for the problem of converting multiple molecule mrv input into jpeg.

Jon