Name to struct command line interface

To Whom it may concern.

I have been working with the name to struct feature of (MarvinBeans) MarvinSketch, which is to say that I have imported IUPAC names into MarvinSketch. I have a fairly large number of chemical names to try and it is wuite conbersome to do this on the MarvinSketch UI.

Is there a way to interact at the command line nevel with the Name to Struct Feature?

Thank you.

Dear Alfredo,

 

According to http://www.chemaxon.com/forum/ftopic4036.html either MarvinView or the command line molconvert tool is capable of mass convert multiple structures.

If you have any further questions do not hesitate to ask them.

Regards,

Gabor

I have gone through your molconvert options and I could not find the proper options to convert a file with chemical names ( mostly IUPAC names ) into smiles for instance.

I understand that MarvinView can be used by opening a .names file, I have actually done this succesfully with pure IUPAC names, however that process requires a full UI to be used.  I am looking for a command line version of the .names MarvinView conversion process.

Gabor,

I tried the commandline version with molconvert and got the following error.

Commands I used:

molconvert name C6H6.smi > C6H6.name

creates a name file

benzene
3-(cycloprop-2-en-1-yl)cycloprop-1-ene
bicyclo[2.2.0]hexa-2,5-diene
tricyclo[3.1.0.0^{2,6}]hex-3-ene
prismane
tetracyclo[2.2.0.0^{2,5}.0^{3,6}]hexane
hexa-1,3-dien-5-yne
...snip

But the reverse with

molconvert smiles C6H6.name

Creates an error with licensing (I have a full academic LIC) with MarvinSketch 5.1.3_2

and the IUPAC naming license working under the GUI.

Z:\>molconvert smiles C6H6.name
C6H6.name:1: error: No valid license has been found.
Product name: Name to Structure
License path: C:\Documents and Settings\XXXXX\chemaxon\license.cxl
Please contact sales _at_ chemaxon.com to obtain the corresponding license.
Students and academic researchers are entitled of free use
through our Academic Package, for more information
please visit: http://www.chemaxon.com/acpack_conditions.html />chemaxon.license.LicenseException: No valid license has been found.
Product name: Name to Structure
License path: C:\Documents and Settings\XXXXX\chemaxon\license.cxl
Please contact sales _at_ chemaxon.com to obtain the corresponding license.
Students and academic researchers are entitled of free use
through our Academic Package, for more information
please visit: http://www.chemaxon.com/acpack_conditions.html /> at chemaxon.license.LicenseHandler.checkLicense(LicenseHandler.java:402)
at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.checkLicense(IUPACNameReader.java:159)
at chemaxon.marvin.io.formats.name.nameimport.IUPACNameReader.importName(IUPACNameReader.java:44)
at chemaxon.marvin.io.formats.name.NameImport.readMol(NameImport.java:39)
at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:170)
at chemaxon.formats.MolImporter.readDoc(MolImporter.java:705)
at chemaxon.formats.MolConverter.readDoc(MolConverter.java:794)
at chemaxon.formats.MolConverter.convert0(MolConverter.java:708)
at chemaxon.formats.MolConverter.convert(MolConverter.java:660)
at chemaxon.formats.MolConverter.main(MolConverter.java:1560)

 

Could you check that please? Thank you!

Cheers

Tobias

 

 

Dear Alfredo,

 

Molconvert handles input containing names like other formats:

molconvert smiles names.txt

Please note that "name to structure" license is required for this operation.

 

Regards,

Gabor

 

 

Dear Tobias,

 

I will forward your question to my colleague who deals with license issues.

 

Regards,

Gabor

Dear Tobias,

you may need to update the license file.

IUPAC Naming license is an older license (for versions prior to 5.1) and it covers the Structure to Name functionality only.

For Name to Structure a separate license is required called "Name to Structure". (You can check if you have a valid N2S license for example in the License Manager GUI.) If you only have a "IUPAC Naming Plugin" license you need to update the license file.

Kind regards,
Judit

Hi Judith and Gabor,

thanks alot, I updated the license and it works.

 

molconvert name C6H6.smi > C6H6.name
molconvert smiles C6H6.name >c6h6-name2structure.smi

The conversion name to structure to name works fine.

I attached all files as smiles and txt and the proof using the inchikey equality test.

Tobias

 

 

..moved to naming forum (tobias)