cxcalc -S name using traditional names?

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

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.

Usage:
  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).

Example:
  cxcalc name test.sdf

Zsolt

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: chemaxon.marvin.io.MolExportException: Name generation failed: chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$UnsupportedError: Naming is not supported on this structure: Multiple radicals are not supported

 

  Marvin  06281022462D 

 

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.

Zsolt

How does one access structure to name via java API?

 

mol.toFormat("name");

See

1. http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/struc/Molecule.html#toFormat(java.lang.String)

2. http://www.chemaxon.com/marvin/help/formats/iupac-doc.html