Template based depiction

Hi,





I don't know if this is something that exists already, i had a quick look at standardizer but couldn't find this functionality....





Essentially we have a set of structures from a virtual library and we have a specific way we want them depicted based on the core template. So, we want the core to be depicted based on our template then the rest of the molecule depicted by JChem. I have seen some of your code for doing a similar thing by doing to sub-structure search then aligning based on the hit using MolHandlers align method, but this only changes the rotation of the target molecule.





Any ideas ?





Many thanks


Alistair

We do not have this functionality yet but we will add it in the next major (non-bug-fix-only) release. We are currently working on partial clean of molecules which is nearly ready. We are planning to implement this relative clean function as a combination of substructure search, atom coordinate copy from query (template) to target, and finally partial clean with fixed scaffold (scaffold = template image in target). We will add this both as a separate module and as an action in Standardizer.





Do you have any suggestion for the name?


What we currently have in mind is "RelativeCleaner" but there may be a better idea.

Hi,





I was wondering if this been implemented ? If so, is it part of the Standarizer ?





Thanks


Alistair

Yes, it is included in the latest Jchem 3.1.1. See


http://www.chemaxon.com/jchem/doc/user/Standardizer.html


http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#cleansec


for details.

Fantastic!





Many thanks


Alistair