CAS number to structure - [Na]

Hello,

I seem to run into some very odd issues when using MarvinSketch Name to Structure plugins, but these effects are also applicable to MolConvert.

When I try to enter a CAS number into ChemAxon, it does not result a structure, but rather a single ion. In this case, it is often sodium since the compound is a sodium salt. For example, the compound sodium vinylsulphonate (CAS number: 3039-83-6) will not return a proper compound when imported from the CAS number.

 

Then, when doing the same thing with the real name:

Clearly, the CAS number import does something horribly wrong. Why am I only getting sodium returned? This happens for some (like calcium diformate), but not all compounds, which is what puzzles me. For example, it doesn't happen to the salt of Methallylsulphonic acid (CAS: 1561-92-8) 

 

Do you have any lead why this nonspecific behaviour is present?

 

Regards,

Eelco

Hello,

I get the correct answer for this CAS number. I see that your are using the latest version. However, CAS number results are cached, and it's possible that an older version returned a wrong result, since there have been changes recently.

Could you please quit MarvinSketch then delete the file C:\Users\<USER>\ChemAxon\naming\cas.cache ?

Do you get the same result afterwards?

Best,

Daniel

dbonniot wrote:

Hello, I get the correct answer for this CAS number. I see that your are using the latest version. However, CAS number results are cached, and it's possible that an older version returned a wrong result, since there have been changes recently. Could you please quit MarvinSketch then delete the file C:\Users\<USER>\ChemAxon\naming\cas.cache ? Do you get the same result afterwards? Best, Daniel

Hello Daniel,

 

Thank you for the rapid response. I have tried your suggestion, but it had no effect. I deleted the cache as requested and, while the import time was significantly longer, it still resulted in the first image shown in the original post.

I rechecked the CACHE file and it "correctly" pasted the value to it:

3039-83-6 [Na]

So, in all, this seems not to be a problem with the cache file. Any other suggestions I can try? I updated my software this morning in the hope that it would remedy the problem but it seems not to.

Regards,

Eelco

Thank you for trying it. Which version of Java are you using?

dbonniot wrote:

Thank you for trying it. Which version of Java are you using?

Hello Daniel,

I am using Java 1.8.0_91.

Kind regards,

Eelco

Hello,

I was wondering if there is already more information available on a possible fix or work-around? It is quite burdensome to find these erroneous entries in a database of 5000 compounds. I have completely uninstalled and reinstalled Marvin and it did not alleviate the problem, giving similar results as before.

It's not limited to software interface as well, since even the MolConvert command line gives the same results.

Is there anything else I can try?

Regards,

Eelco

Hi Eelco,

I understand and am sorry about your difficulties. Unfortunately CAS makes it intentionally difficult to process CAS numbers unless you pay them and use their own solutions. We would be happy to provide better integration but so far they have not allowed it.

Would you be open to follow some technical instructions to enable some low-level logging, so we can understand what is happening on your system?

Best  regards,

Daniel

dbonniot wrote:

Hi Eelco, I understand and am sorry about your difficulties. Unfortunately CAS makes it intentionally difficult to process CAS numbers unless you pay them and use their own solutions. We would be happy to provide better integration but so far they have not allowed it. Would you be open to follow some technical instructions to enable some low-level logging, so we can understand what is happening on your system? Best  regards, Daniel

Hello Daniel,

I completely agree on the difficulty of CAS, and I ideally avoid them, but the person who constructed the original database thought CAS was a good idea. I've managed a few workarounds for the current database, but I will have more & larger data in the future that needs processing.

That said, I'm open to machine logging to understand the issue. If not to solve the issue, then to satisfy my curiosity why this happens.

Best regards,

Eelco

I sent some instructions by email.

Daniel