how does template clean matching work?

Hi,

 

I use the clean2d action of the chemaxon standardizer. For some of my structures I need to do template based clean.

In the most cases my (custom) templates are matched and clean does retain the coordinates of the atoms/bonds defined in my template.

There is one group of structure where I have difficulties to match my template. Those are 'ferrocene like'structures i.e. Cp rings connected to Metal atoms such as Iron etc.

An example is attached to the post.

Question: For the structure in the image attached- What is the MINIMAL template (defined as molfile) I need to define to clean the structure (e.g. straighten the CO groups) but RETAIN the 'pseudo3d' look.

with other words: How does template based clean2d tries to match the (custom) templates (in my case defined in an external SDFile) in the original structure? Is it a substructure match or something else?

In the same context: Since I might have other similar structures where the metal atom is not Iron , but eg. Chrome:

Can I use query atoms (A or Q) or e.g. atom lists in my template?

Hope one help. Thanks for feedback in advance.

Best regards

Hans-Juergen

 

Yes, query atoms and query bonds can be used in the template. I have attached an example which uses only carbon atoms, any atoms, and any bonds.