openmolecules.org Forum: Functionality » Aligning molecules to a common substructure

Home » DataWarrior » Functionality » Aligning molecules to a common substructure

Show: Today's Messages :: Polls :: Message Navigator

Aligning molecules to a common substructure [message #644]

Sat, 05 October 2019 03:05

sbembenek18
Messages: 62
Registered: April 2019

Member

Is it possible to align all the molecules to a common substructure?

Report message to a moderator

Re: Aligning molecules to a common substructure [message #651 is a reply to message #644]

Mon, 07 October 2019 00:02

nbehrnd
Messages: 235
Registered: June 2019

Senior Member

Please indicate if I'm wrong, but I understand your case like aiming to sort molecules
featuring the same core substructure in groups together. If so, I suggest to try
Chemistry -> Analyse Scaffolds -> Murcko scaffold. This will add a new column which
equally allows sorting of the data set, e.g. to alter a sort by structure (here, the
first column):

index.php?t=getfile&id=115&private=0

by a sorting according to the Murcko scaffold (here the third column):

index.php?t=getfile&id=116&private=0

As usual, the header of the column (e.g., the third one) may be renamed to your needs.
Note, the manual includes an illustrated definition about different scaffold criteria
available to you ( http://www.openmolecules.org/help/chemistry.html#ScaffoldAna lysis).

Norwid

Attachment: sort_structure.png
(Size: 6.16KB, Downloaded 1106 times)
Attachment: sort_MurckoScaffold.png
(Size: 6.03KB, Downloaded 1152 times)

Report message to a moderator

Re: Aligning molecules to a common substructure [message #655 is a reply to message #651]

Wed, 09 October 2019 23:17

thomas
Messages: 741
Registered: June 2014

Senior Member

You can generate new atom coordinates with:

"Chemistry -> Generate 2D Atom Coordinates"

Then check

"Automatically detect scaffolds and unify their orientation"
and select a scaffold detection method: "most central" should be fine

When clicking OK, DataWarrior will rearrange your 2D-structures such that the most central ring system, where multiple molecule share the same scaffold, this scaffold is always drawn the same way.

For more flexibility, you may provide scaffolds with defined coordinates in the same dialog.

Report message to a moderator

Re: Aligning molecules to a common substructure [message #664 is a reply to message #651]

Fri, 11 October 2019 18:48

sbembenek18
Messages: 62
Registered: April 2019

Member

thanks!

Report message to a moderator

Previous Topic:	New feature request: align structures
Next Topic:	Conformers and xyz

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Thu Jan 15 10:26:21 CET 2026

Total time taken to generate the page: 0.71369 seconds