Standardizer API function to replicate Marvin Clean in 2D?

Hi,

Is there a standardizer command in Java API to replicate effect of Marvin Clean in 2D (MarvinSketch version 14.10.27.0)?  We are using Chemaxon Java API 14.10.13.0.

I thought it would be:

     Standardizer standardizer_clean = new Standardizer("clean");

     standardizer_clean.standardize(mol_pc);

Use

Standardizer standardizer_clean = new Standardizer("clean2d:full");

for now.

There is a new 2D clean algorithm which haven't been fully integrated into Standardizer yet, so the result may differ from what you get in MarvinSketch. According to our plans Standardizer will start using the new 2D clean algorithm in few weeks. 

Thank you for the quick reply.

Our API version seems to only respond to "clean:full", not "clean2d:full".

So there is currently no API way to achieve partial clean ( that only reorients least amount of structure necessary .. like in "Partial Clean" top row of this page https://docs.chemaxon.com/display/standardizer/Clean+2D )?

Andrew

In the current version of Standardizer partial clean does not work. It is a bug, and it will be fixed in JChem version 15.01.19. (it will be released in 1-2 days).

Partial clean also can be achieved with the Cleaner class from the JChem API.

Thank you for the information.

Best,

Andrew