creation of 3D structure using action strings

Hello:


I would like to use action strings with the standardizer to do several things to a mol file including keep the largest fragment and convert a 2D structure to a 3D structure. I tried using ..clean:3.. and ..clean:full:3.. in the action string, but these did not work. Is there a way to do this?


Thanks.


John

Currently 3D clean is only available in the XML configuration but I will add this to the action string for the next major JChem release (JChem 3.2).





I attach an XML config example, you can run it by:

Code:

standardize -c st.xml test.mol -f mol -o o.mol

If you use the Standardizer API from a JAVA program then you can also give an XML string as well as an action string in the constructor.

From JChem 3.2 version you can use the following action strings:

Code:

- "clean:3" (clean in 3D) - "keepone" (largest atom count) - "keepone:mass" (largest mass)

With JChem 3.2 we have released a Standardizer GUI application, which makes the usage of Standardizer even more easier.





Check the Standardizer User's Guide for more information.





Best regards,


Zsolt