Beautifull structure orientation

Hi everyone,


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!!



Hello, Lionel

It is possible to implement such functionallity, but some examples would be helpfull.

What should be done in case you have a chain template CCCCCCCCC, and want to aligh a circle C1CCCCCCCCCC1? What kind of templates do you have?

Best regards,

Hi Mikhail,


Join you have a workflow with one example. Here the structures are based on the same heterocycle. I think this is the principal case.

So here you can see that the structures have not the same :

- general orientation

- orientation of the CH2-O group

- orientation of the C(=O)-O group


For your question, I think that I dont want to align a chain template on a circle for THIS use.


Best regards


This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.