I use the chemaxon standardizer to perform 'partial' clean2d operations.
The aim is to 'straighten' non linear triple bonds such as in case of cyanides.
This works pretty well. In some cases I realized that beside of cleaning the coordinates of atoms/bonds inside the CN group, there are additional changes done to the molecule. This happens if certain templates are present in the molecule e.g. a bicyclic ring is present. The layout of this templates gets changed. I attached an example to this forum post.
Obviously there exists (in the chemaxon environment) a library of templates that standardizer tries to match when performing a clean operation, and if present, forces the layout of the mapped atoms/bonds in the input molecule to follow the layout defined in the template.
Question: Is there a way to prevent that this happens?
Hope one can help.
Thanks for feedback in advance.