One collegue ask me this question:
I have a series of molecule with the same template with differents or common groups and attachement points. The structure were drawn from differents place so with differents orientations: Ph up in the first structure, down in the second, ... I would like to recompute the 2D coordinates of the structures to have the same orientation of the template for all the molecules AND of the groupements in common in a subset. All in order to compare rapidly the structures.
How to do this?
I tried to recompute the coordinates but not efficient. I tried to draw the template, search the template in a "substructure matcher" with the option "align structure" but the alignement is a "mean" alignement and not recompute/change the coordinates.
So, any ideas are welcomed!!