cxcalc -S name using traditional names?

User 1a3b6cd85b

29-06-2010 05:13:48

Is there a way to use cxcalc to generate traditional names in batch?


This does not seem to work:

cxcalc -S name:t  mySDFile.sdf


While, this works as expected:

molconvert name:t mySDFile.sdf

ChemAxon e08c317633

29-06-2010 10:54:03

Yes, there is.

The correct syntax is:

cxcalc name -t traditional mySDFile.sdf

Command line help:

cxcalc name -h

Calculator plugin: name.

Generates the IUPAC name of the molecule.

cxcalc [general options] [input files/strings] name
[name options] [input files/strings]

name options:
-h, --help this help message
-t, --type [preferred|traditional] (default: preferred)
preferred: Preferred IUPAC Name
traditional: traditional name

Multiple values for the same parameter should be
quoted and separated by commas without space
(e.g.: -t "v1,v2,v3" where v1, v2, v3
are the specified values of parameter t).

cxcalc name test.sdf


User 1a3b6cd85b

29-06-2010 17:58:03

Very helpful, thanks. Missed that!

On a different note, how can the error messages be supressed when a name can not be generated? I am trying the -S switch, but the errors get added into the sdfile causing subsequent problems:

An example error is, it seems to get added near at the top of the molfile segment - e.g.





293     name: Name generation failed:$UnsupportedError: Naming is not supported on this structure: Multiple radicals are not supported


  Marvin  06281022462D 


ChemAxon e08c317633

30-06-2010 22:41:26

Error messages are written to the standard error channel (System.err), so they will not appear in the molfile.

If the error message appears in your molfile, then please specify the full command you used, and attach the molfile you got.


User 1a3b6cd85b

10-08-2010 19:09:56

How does one access structure to name via java API?

ChemAxon e08c317633

11-08-2010 06:43:49