Beautifull structure orientation

Community Extensions Indigo
#1

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!!

 

Lionel

#2

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,
Mikhail

#3

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

Lionel