IUPACNamingPlugin and strange characters in generated name

Dear ChemAxon community,

I am using the IUPACNamingPlugin to generate IUPAC names from MOL files.

In some cases - ex. the attached one - the generated IUPAC name contains strange characters. For the attached structure:

(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2$l^{5},4$l^{5}-trioxadiphosphocane-2,4-bis(olate)

Any ideas about what's happening? Thanks in advance,

 

Rafael

Dear Rafeal,

What you are seeing is the "lambda notation". Since the two phosphorus have the non-standard valence 5 (and not 3), this is marked in the name with a λ⁵. The current ascii representation for this is $l^{5}. If you run the Tools/Naming plugin in mview or msketch you will see the lambdas. Additionally, you can get the unicode string representation on the command-line (molconvert) or the API using the name:u format option (u stands for unicode), which will give you:

(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2λ⁵,4λ⁵-trioxadiphosphocane-2,4-bis(olate)

 

Which usage concerns you, and would you require some changes?

Best regards,

Daniel Bonniot

Thanks for the response, it clarifies the issue. Sorry about my ignorance about lambda notation.

We need ASCII names (not unicode), so perhaps I should try getting the traditional IUPAC name?

Thanks again,

Rafael

If you need pure ASCII names, then the version you wrote first, with $l^{5}, is correct. Is there a problem with that?

Hi,

Is there any plan to provide support for obtaining the unicode string, with lambda characters et al, from the IUPACNamingPlugin plugin so that getPreferredIUPACName() and getTraditionalName() can be called with the same results as calling MolExporter.exportToFormat(cxMolecule, "name:u")?

Regards,

Nathan

Hi Nathan,

Since 5.11, the unicode output is the default.

Otherwise, is there any inconvenient to use MolExporter instead of the plugin?

Daniel

Hi Daniel,

Thanks for the info. I upgraded the version of library to 5.11 and it works fine.

Thanks,

Nathan

Dear,

we are wondering if it is possible to get the name without the special character like $l^{5} or λ⁵ by your Naming Plugin.  We would like to
have a name with standard characters that can be parsed by standard drawing
packages.  We use the names for patent applications and they need to make
sense to the medicinal chemistry community.

Thank you very much

Dear Juan,

Thank you for your feedback. I understand the "$l" notation is not ideal when a readable form without special characters is desired (for the record, I think major drawing tool also understand the $l form).

Therefore we have decided to switch to using "lambda5" when using the ASCII option (the default remaining to use unicode characters: "λ⁵"). This change should appear in next week's version.

Which method or ChemAxon tool are you using to generate the names?

Dear, 

Thank you for information. We are very happy to hear there is new version to this issue. we are wondering if this new nomenclature with "lambda5" can transfer to the correct structure in the other major drawing like Chemdraw or ISIS draw.

we have structure to name license of ChemAxon to generate the names

Look forward to your new version! 

I can confirm that the new "lambda5" syntax is supported by ChemDraw (as well as the previous "$l^{5}" syntax).

I could not confirm it for ISIS draw since I could not find its option to import names at all, but you can try it by importing "(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate)", or with a simpler name: "pentamethyl-lambda5-phosphane".

Just a confirmation that the current versions use the "lambda5" syntax when using the ASCII option.

dbonniot wrote:

Just a confirmation that the current versions use the "lambda5" syntax when using the ASCII option.

I just downloaded the Marvin Beans with version as 15.4.27.  I got a name like "3-(dimethylamino)-1λ⁶-thiolane-1,1-dione“ about "S" with non-standard valence. Does it need some special setting about "ASCII option” you said? or this new function work from 15.5.4?

Thanks

In Marvin Sketch, you can use the Edit menu, Copy as... and choose "IUPAC name (ASCII)" to copy the name without special characters to the clipboard.

It is also available in command line (MolConverter) and the Java and .Net API using the "name:ascii" format option.

dbonniot wrote:

In Marvin Sketch, you can use the Edit menu, Copy as... and choose "IUPAC name (ASCII)" to copy the name without special characters to the clipboard. It is also available in command line (MolConverter) and the Java and .Net API using the "name:ascii" format option.

It works, thank you very much