Convert name to structure

Dear chemaxon,





I have read forum about about convert name to structure but i don't find a solution for me.





Do you have a tool (a batch program) to convert name to structure ?


I have a lot of compound to convert.





Thanks,





Karim.

Dear Karim,





With Marvin or JChem 5.1, you can do batch conversion of names to structures. In this case name is just an import format, so you can do it as with other formats:





1) Use MarvinView to open a .name file with names in it, one per line, and use Save As... to save the structures.





2) Use the molconvert command line tool.





For batch conversion of names you need a "IUPAC name" license.





Let me know if you have any further question.

Dear Chemaxon,





I want to try marview but i must have a licence key.


Is it possible to have a licence in order to try marvinview please ?





Thanks,





Karim.

Thanks for licence key.





I'm testing marvin view...but I have a problem with convert name to structure (see jpg file).


The structure generate by marvin view is not good.





Do you have an idea about this problem ?





Thanks,





Karim.

This name is a CAS name, which is not yet a well supported nomenclature. Do you have no IUPAC names for your compounds?





In this case the chloro substituent is correctly interpreted, but the next one is ignored. We will look into supporting this name style as well, as soon as possible.

I have no IUPAC name, i have only CAS name.


Do you have a tool to convert CAS to IUPAC ?





Thanks, Karim.

We don't have such a tool at the moment. As I said, we will work on better supporting CAS names (which will of course also make it possible to reexport as IUPAC names if you like).

Can an example ".name" file be provided?

A name file is a plain text file, with one name per line. I attach a very simple example. Note that for temporary technical reasons, the file is called example.txt, which also works since marvin can automatically detect format, but you can rename it to exemple.name.

 

Note that relative to a previous question in this topic, CAS names are now supported.

 

Dear ChemAxon,

I am having some problem converting  an IUPAC to a right structure. The IUPAC name is as follows:

(2’R,3S,4’R,5’R)-6-Chloro-2-isobutyl-2-oxo-4-phenyl-1,2-dihydro-spiro[indole-3,3-pyrrolidine]-5-carboxylic acid dimethylamide

I have tried the following measures:

1) I have tried to open the .name file containing this compound in marvinview and saving it as .smiles and .name. But the files that get written are always empty.

2) I have tried using name import in marvin sketch but apparently it doesn't like the name format as such. However, if I remove the isomer information "(2’R,3S,4’R,5’R)" it produces a wrong compound (different isomer "2’R,3S,4’S,5’R")

3) I have tried using molconvert with the following command: molconvert smiles junk.name -o test.smi

but I get an error message saying: "error: Unrecognized name format: ’R,3S,4’R,5’R)-6-chloro-2-isobutyl-2-oxo-4-phenyl-1,2-dihydro-spiro[indole-3,3-pyrrolidine]-5-carboxylic acid dimethylamide"

I have attached my junk.name file for you to look at. Could you please suggest a way around this problem?

Thanks!

-Chet

Dear Chet,

Thanks for your report. All your methods to convert names are correct. The core issue is that the name as it is written could not be converted.

Firstly, it seems it uses a non-ascii character for the primes. I added support for it, this will be released in future versions (from 5.4.1). Until then, simple ' characters should be used, which gives us:

(2'R,3S,4'R,5'R)-6-Chloro-2-isobutyl-2-oxo-4-phenyl-1,2-dihydro-spiro[indole-3,3-pyrrolidine]-5-carboxylic acid dimethylamide

I believe this name is not correct. For instance, with both isobutyl and oxo substituent to atom with locant 2, which is a carbon atom in a ring, we have a valence 5 carbon! Could it be your source is wrong, or some prime characters were lost in translation?

I believe the correct name might be, for instance:

(2'R,3S,4'R,5'R)-6-Chloro-2'-isobutyl-2-oxo-4'-phenyl-1,2-dihydro-spiro[indole-3,3'-pyrrolidine]-5'-carboxylic acid dimethylamide

Finally, and this is our mistake, we do not seem to interpret the 'dimethylamide' part correctly after an acid. I file this to be fixed as soon as possible.

So given the name:

(2'R,3S,4'R,5'R)-6-Chloro-2'-isobutyl-2-oxo-4'-phenyl-1,2-dihydro-spiro[indole-3,3'-pyrrolidine]-5'-carboxylic acid

we can finally generate a structure, which I attach below.

Let me know if you have further comments or need further assistance.

Cheers,

Daniel

PS: do not hesitate to start a new thread when reporting a new issue or question