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.