webservices convertion stucture to name

Dear,

 

I am already using MarvinJS and the molExport function of the webservices in a web interface. When the user is drawing a structure in MarvinJS, I would like to automatically calculate the name (common and IUPAC) of  the structure that I obtained from MarvinJS.

I found this service "/rest-v0/data/sample/table/ChEBI_lite_3star/detail/4", but it seems that I am not in a way to give the "cd_id" parameters.

Is-there a way to use this service based on a structure data (mrv, mol)? Or is-there an other way to calculate the name of a structure?

 

Thanks, Lionel

Hi Lionel,

All of the calculator services has stateless version where you can provide the structure in the request, for example:

POST /rest-v0/util/calculate/molExport
Content-Type: application/json
{
  "structure": "CCCCCC",
 "parameters": "name"
} 

Which will give you back the name "hexane" and the "structure" element in the request can be of any kind of format!

(https://restdemo.chemaxon.com/apidocs/#molExport)

Regards,
Peter 

Also, there is a dedicated service for your usecase:

POST /rest-v0/util/calculate/names 
Content-Type: application/json
{
   "structure": "CCCCC",
    "parameters" : {
       "inchiAux": false,
       "uniqueSmiles": false
   }
}

This will generate all the common names and also iupac name as well.

Regards,
Peter 

Hi Peter,

 

Thanks for your answer.

It seems that your second solution is working but I have an error message. It seems that I need a specific license to do this structure to name conversion. Can-you confirm-me this?

 

Regards, Lionel

Hi Lionel,

Yes I forgot that, you need naming license for any structure2name or name2structure conversions. Can you please contact our sales?

Regards,
Peter 

Hi Peter,

No problem, I will ask to Annamaria,

Cheers, Lionel

Lionel,

One other option to generate the (most popular) common name is to use the molExport function with the "name:common" parameter. For instance:

POST /rest-v0/util/calculate/molExport
Content-Type: application/json
{
  "structure": "CC(=O)OC1=CC=CC=C1C(O)=O",
  "parameters": "name:common"
}

This will return the name "aspirin".

Daniel

Dear Daniel,

 

Thanks for your solution. This works for me.

 

This works, even if I obtain some strange results:

- for "CCCCC" I obtain "Pentane" for IUPAC and "caswell no. 642AA" for common name. Whereas in MarvinSketch I obtain Pentane for both IUPAC and common name

- for the retinaldehyde structure, I correctly obtain the IUPAC name, but I cannot obtain the common name. Whereas in MarvinSketch, I obtain the same IUPAC name, AND "retinaldehyde" as the common name ("traditional name")

 

Cheers,

 

Lionel

Dear Lionel,

Good to hear this works. Regarding the issues:

- for the first one, my mistake, you should use "name:t" (t for traditional) instead of "name:common"

- for the second one, this is an issue in the webservice implementation that we just discovered as well and will fix. In the mean time, a workaround is to use "name:i" (i for IUPAC) instead of "name"

Cheers,

Daniel

The "name:t" is great, and also work for retinaldehyde.

This is perfect, Thanks!

Lionel