Naming of compounds

Dear,

 

We use the structure to Name function of MarvinSketch. And we discovered that the names calculated from "Place IUPAC Name" or from "Generate Name..." are not strictly the same. We found that the dash "-" character is not the same between both option. In the first one it is the normal dash, in the second one it is the hyphen dash (u+2010).

Example:

[1,1'-bipyrrolidine]-2-one
[1,1'‐bipyrrolidine]‐2‐one

I think that the normal dash is less problematic than the hyphen.

Maybe this happen with others characters? I do not know.

 

Lionel

Hello Lionel,

Structure to name always uses the same character, so we have to explore this issue more deeply. Thanks for reporting. Will keep you posted. 

BR,

Krisztian

Hi Lionell,

 

I was not able to reproduce this issue  with the new version of MarvinSketch. One of my colleague checked the code and we call exactly the same function in both cases. However, it could have been some difference in the very first implementation of the analysis box. Could you double check it again  please, and if it still the case could you let  us know a bit more about your environment (operation system, java version etc.)

Thank you,

Efi

Hi Efi,

 

I checked again and still have the issue. I explain:

1- I draw a molecule and select it

2- I use the menu "Calculation/Naming" and either the IUPAC or Traditionnal naming. I obtain a pop-up window in which I select and copy paste the result name in a bloc-notes (txt) document or a Notepad++ document

3- I am doing ctrl-I to obtain the analysis box. I use the "Text" function to select the name and I copy paste it in the text documents.

4- I obtain in Bloc-notes

[2,2'‐bipyrrolidine]‐3‐one (Pref)
[2,2'‐bipyrrolidine]‐3‐one (Trad)
[2,2'-bipyrrolidine]-3-one (Analysis box)

There is a small difference between Pref/Trad result and the Analysis box result

And in Notepad++ (more self explanatory)

 

I am on Windows 7 64 bits.

I am using the 16.5.2.0 version for windows and jre included

 

For me it is a problem of characters encoding or something around that.

 

Cheers, Lionel

Thank you for the clarification, I am adding this new info to our task.

Best regards,

Efi