Name to structure

Hi,

 

I have a couple of questions about the name to structure.

 

Does this run locally or is it a web service?

What is the data source for the names and structures?

 

If I want to use a custom webservice, I'm not clear how to invoke it rather than the ChemAxon name to structure service?

Cheers,

 

Chris

Hi Chris,

Name to structure runs locally. We have our own algorithm for converting IUPAC and systematic names, and our dictionary compiled from several sources for common and drug names.

If you want to use your own webservice, you can configure that in Marvin Sketch or View (starting from version 5.12, which is just released). Select the Edit/Preferences menu, go to tab Save/Load, and fill in the "Name import service URL" field.

You can consult the documentation for the naming webservice for more information.

Best regards,

Daniel

Hi,

Many thanks for the rapid response

I was thinking of testing this facility using the Chemical identifier resolver (http://cactus.nci.nih.gov/chemical/structure), this requires a URL in this format

http://cactus.nci.nih.gov/chemical/structure/ class="highlighted_span highlighted_span_1" style="margin: 0px; padding: 0px; color: #000000; text-align: center; border: 0px 0px 3px dotted #a50021;">"structure identifier"/representation

So return a SMILES for aspirin it would be

http://cactus.nci.nih.gov/chemical/structure/ class="highlighted_span highlighted_span_1" style="margin: 0px; padding: 0px; color: #000000; text-align: center; border: 0px 0px 3px dotted #a50021;">aspirin/SMILES

Would this be possible?

Can I then use this from within Marvin sketch?

 

Cheers,

Chris

Hi,

That's a very good idea. Unfortunately currently we only support URLs that have the name at the end, because it was simpler and we thought of people writing their own service. But this shows we need to support the general case. I marked this as a task for a future release.

Until then, you would need to test it using another webservice that accepts this format, or write your own service (which could be just a proxy delegating to another service).

Daniel

Hi,

 

Ok I set up a web service to do this and it works fine. 

I wonder if it might be useful to have some way of making sure the user knows which service they are using before sending off information?

Cheers,

Chris

http://www.macinchem.org

That was quick :) Glad to know it works for you.

Are you concerned about confidentiality? Our assumption is that if a user explicitly sets up a webservice to be used, they are aware it will receive the information and they are OK with that.

Security is one concern, but I can imagine instances where users might get unexpected results depending on the service that is being used.

I've done a little more experimentation and it works fine unless there is a space in the identifier, perhaps it needs to be url encoded?

I understand. Currently we assume the user is aware of the configuration they have made for the webservice in use.

You are absolutely right about URL encoding, it was missing. I added that. I also allowed the URL to contain a [NAME] marker to support having the name in the middle of the URL. Both improvements will be released with the next major version: 6.0.

Just thought you might like to see I've written up my experimentations here.

 

http://www.macinchem.org/reviews/marvin/marvinWebservice.php

 

Cheers,

 

Chris

Chris,

Great, thanks for the review(s)! The code for the related improvements is already in place in the 6.0 branch :)

Cheers,

Daniel