converting to inchi with key but without AuxInfo

I need to convert SDFiles to inchi, I need InchiKey as well but not the AuxInfo. I am running the following command:

molconvert -g inchi:AuxNone,key "inputfile.sdf" -o outputfile.inchi

receiving error message "key: not found"

What is wrong ?

Thanks

Jiri

Hi,

I have tried the following 

First made a simple sdf:

molconvert sdf -s "CCO" -o cco.sdf

Then used Your command:

molconvert -g inchi:AuxNone,key cco.sdf

>InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3

>InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N

It works on my machine, please tell us the operating system, java version, and Marvin version on Your computer. Maybe you are using an old version of Marvin before we added the inchi key function. You can check this by using the molconvert without parameters, and check that both inchi and inchikey is on the list:

$ molconvert

Molecule File Converter, version 5.3.1, (C) 1999-2010 ChemAxon Ltd.

Usage: molconvert [options] outformat[:export-opts] [files...]

Converts the specified files to another format.

  Output molecule formats: mrv, cxsmiles, cxsmarts, abbrevgroup, csmol, csrxn,

    cssdf, csrdf, mol, rgf, mol:V3, rxn, rxn:V3, sdf, rdf, cml, cdx, smiles,

    smarts, inchi, inchikey, name, peptide:1, peptide:3, mol2, sybyl, pdb, xyz,

    cube, gjf.

Best Regards,

Peter

I guess that Jiri uses Windows and launch MolConverter with the molconvert.bat batch script. Can you confirm it?

C:\Program Files\ChemAxon>MarvinBeans\bin\molconvert.bat sdf -s "CCO" -o cco.sdf

C:\Program Files\ChemAxon>MarvinBeans\bin\molconvert.bat -g inchi:AuxNone,key cco.sdf
key: not found

Unfortunatelly, batch scripts can not accept comma (,) in command line statement.

In the batch script lanuage, comma is separator character. The batch script determines parameters like this:

• param1=-g


• param2=inchi:AuxNone


• param3=key


• param4=cco.sdf

Unfortunatelly, there is no way to escape comma in batch script language. It is the shortcomming of this technology.

I can recommend the following workaround:

• Call java class directly (no linebreak in the statement):

java -classpath "C:\Program Files\ChemAxon\MarvinBeans\lib\MarvinBeans.jar" chemaxon.formats.MolConverter -g inchi:AuxNone,key cco.sdf

• Use the platform independent version of Marvin (marvinbeans-VERSION.zip). It includes unix like shell scripts. To be able to launch it, CygWin has to be installed to your machine. Unix shell is more flexible than batch script language. Unix shell scripts accept comma in statement.


• We can provide a Windows Shell Script to launch MolConverter. It is not part of the Marvin Beans package but you can download it from here. About molconvert
  In this topic, the Windows Shell script is attached and you can find more details about the above issue.

Tamas is right, I am running the molconvert directly from the windows command line. Thanks for the suggestion but it somehow exceeds the level of my technology skills. For now I will run the command using the "inchi:key" specification and simly delete the unwanted auxiliary info from the results (talking about 5 million+ molecules, ufff).