Aromatic rings

Hi

I am using a KNIME (2.7) workflow with Marvin nodes to generate an SD file that I can use to register structures to our database. I have also used JChem extension in Excel (5.10.0.673) to generate the SD file as well. We use IDBS Activity base and Selection assistant to register structures which are on a Citrix server. Unfortunately, we do not have the Marvin suite installed on this server so the structures are rendered with ChemDraw Ultra 11.0.

When importing the SDfile into this software, it has issues dealing with the aromatic rings. The software requires the structures to appear in simple bond formats (i.e. single and double bonds). ActivityBase reads the structure and determines the aromaticity for itself. The files should be saved in a format where they contain the explicit bonds. I am having to manually correct the structures in ChemDraw. Does any one have any ideas how I can get around this issue?

Regards

Alexandra

 

Dear Alexandra,

If you use a MolConverter node, add "-a" to the export options, it will convert the stuctures to Kekule form.

You can achieve the same functionality with a Standardizer node.

If there is no such node in your workflow at the moment, you can simply add one.

Best regards,

Peter

gezapeti wrote:

Dear Alexandra, If you use a MolConverter node, add "-a" to the export options, it will convert the stuctures to Kekule form. You can achieve the same functionality with a Standardizer node. If there is no such node in your workflow at the moment, you can simply add one. Best regards, Peter

Dear Peter

Thank you so much. That worked perfectly!

Regards

Alex